(after having typed all this, I see how long it got... I don't blame anyone for not wanting to read/comment on it)
Arthmoor: It seems you are very opinionated, and not afraid to impose those opinions on others with brute force (http://www.gamesas.com/topic/1352954-unofficial-creation-kit-modding-bug-list-3/page__st__60). In that thread you argue with someone over making BSAs in the CK; making a point that I tried to make in this navMesh thread a while back... that isolated incidents may not constitute a universal bug. If I can get my mod (and others) working fine, but you and MAYBE a couple ISOLATED others (post v1.526) still cannot, it seems you should take your own advice. How many people have added back their navMesh and still get bugs (like the balcony thing)? How many tried doing things they should've learned more about before doing them?
I advocate politely voicing opinions... until enough people speak out (lobby) and are noticed to cause action to be taken - the action I was suggesting was allowing more file-types on the Workshop, not to abandon it altogether. Personally, I've never used Skyrim modman software or Workshop - mainly because of all the limitations, potential bugs, etc they come with... so perilous abandonment isn't an issue with me. Although.. I did say abandonment was an option - but for those people who aren't willing to 'contort' themselves for the 2min it takes to make a working ESM (or those not willing to upload an incomplete mod).
3rd party software is NEEDED to make certain mods, and ALWAYS will be - as some 1st or 3rd party software Ma Beth uses in their dev is proprietary and hacked out of the CK before public release. The public will never have the exact tools used to make the game itself, and must find viable workarounds to fill those 'spaces' back in. On this point, I agree with Amethyst Deceiver that your seemingly unique perspective labels ALL texture and mesh replacers as 'illegitimate hacks', certainly a valid statement when viewed from a purist. (so I expect you've removed your nvdey mod by now... as not to advlterate your gaming experience; no pun intended)
The navMesh issue may be ONE example of this. If Ma Beth's CK can create ESMs and make/edit all their data with it, yet the public version cannot... has it occurred to you that the 'fix' to this ESM thing is proprietary and will NEVER be implemented? They seem to have acquired rights to distribute the facegen aspects of the CK (ie: lip synch, which was removed as proprietary for Obliv as I recall), and there are 'bugs' with THAT are there not? It has been shown the grey-face bug is NOT a bug, but a limitation... which people still claim as a bug and still demand it be rectified. I think you (and others) may be demanding the same for ESMs and/or other aspects of the CK. It could be that in their trying to workaround such legalities, they triggered the bridezilla CTD bug; WHICH by the way, lessens my hope/faith that a fix is imminent where your hope is bolstered - as they rolled back their changes... implying that they have to start over again (or in part), or a little hot-fix could have been released.. not a 'complete' roll-back.
While I don't use the method personally, one supposedly does NOT need 3rd party software to make an ESM. While I haven't tested it, there have been plenty of anecdotes relating how to do it the CK itself (even in this/last thread as I recall).... make your areas, save it to ESP, exit CK, rename ESP to ESM, reload in CK (or something to that effect). Had it occurred to you that this method may NOT be a hack, but the way Beth folks have to do it? (though I doubt it, as they still have to 'snip' over changes from ESPs into the master Skyrim.ESM) But none of this helps YOU, as the mod I believe you have trouble with is Open Cities... which doesn't need an ESM (as it already has one... Skyrim.esm).
By the way - using Snip or other software doesn't change the way the game handles data files, it only changes the data in those files... the game still uses the file the same way it always has (albeit in a potentially buggy finished product, caused by the strange data not the game-engine). But I'm sure you knew that already.
I'm dismissive of many INSTANCES of this navMesh thing, as I personally believe many can be rectified through proper modding and using the correct software (not GECK/FO3 stuff). I'm not dismissive of people, opinions, and their problems (as you are in this and other threads), I try to help as best I know how. If it means showing you working mods (eg: my real mod, and the test ESP in this/last thread) and explaining how I did it - then showing how others' method differs or may be problematic, I have no idea how that is dismissive.
I know Amethyst Deceiver unsuccessfully tried the older version of my Tower mod with v1.524 (CTD), but has anyone tried my new version (1.81b) with Sky's new version (1.526)? I replaced all the Vanilla navMesh and hooked it all up like before... works fine for me. No balcony, no NPCs in corners, followers correctly escort, etc etc. This is with over a dozen Vanilla cities/villages navMesh altered, linked to custom interiorCells; as well as a couple exterior Vanilla cells which didn't have navMesh before (as your mod does).
Which brings me to this... I downloaded and tried your mod. As expected, MOST of the NPCs in Riften were on the balcony... but not all. There were still a few NPCs, like one by the gate, another down the lane a ways, etc. I loaded the mod in the CK, and there were several errors - a couple right at startup (besides the Vanilla errors) and some when loading the Riften cells. I don't recall off-hand what the errors were, but I'm sure you're aware of them already... if not, your CK is corrupt and is likely the ultimate source of your problems.
If the errors are truly benign (which I doubt, as at least one was navMesh-related I think), then disregard this paragraph. My Overlook Tower mod has minable Salt and respawning Nirnroot... I did this by creating new Tree objects using static NIFs; but when loading the area they are placed in, CK shows treeLOD errors (or something like that). THOSE are benign errors, as CK is looking for data in the NIF which isn't there, yet it only affects cosmetics in-game; YOUR errors may not be so passive...
My point is that you, yourself (in another thread), chastise someone for complaining about a buggy mod when the CK showed errors in it. That thread is like the polar opposite to this one, as there you advocate that 'corrupt data' causes drama (yet here 'corrupt' is a bad word), etc etc... many of the things which I have posted about here you've denounced, but advocate in other threads. Seems you should run for the American presidency on the flip-flopper ticket. I read that thread a few days ago, and I tried to go back and find it to link to, but I gave up standing in front of the wall of posts... so sorry, I cannot cite which thread I'm talking about (I'm sure you would recall, as you were as adamant in that thread as you are here... though the exact opposite stance).
As for my "magic" - I told you how I did it, the same way we modders have been doing it for like five years now... nothing magic, nothing local to my machine. I even posted a video and ESP proving it works ; though that vid was with Sky v1.4, the process and results are the same with Sky v1.526. The ESP is still in Dropbox BTW... in case you wanted to try it in v1.526. SOOOOO.... unless you can fix those strange errors the CK spits out just by loading your mod and modded areas, I doubt you'll have luck getting it to work correctly in-game.
Now, for constructive advice - my opinion is that you tried to bite off more than you should've for that mod's release. Starting with ONE city, and getting it to work flawlessly, would have been my modus operandi... there are WAY too many aspects in Skyrim to just 'cut & paste' an entire city to a new location (as one may have done in the past..). Too many triggers, scenes, markers, scripts (and their assigned references/properties), etc etc... to expect to get all that working flawlessly in a 'spliced' Vanilla city is fairly unrealistic (in MY opinion).
Hell, I tried simply re-finalizing Ivarstead's navMesh (without ANY changes/additions whatsoever), and it destroyed/corrupted the entire town's navMesh beyond all recognition... but when I tried it by just loading Skyrim.ESM in the CK (then finalize Ivarstead) it works normally. I also just tried adding it back into my mod (just now), semi-successfully... it still had 7 tri-errors (edges not lining up I think), but they were they in Vanilla. So this scenario implies that one of my CK SESSIONS corrupted the navMesh. Before you blindly berate that statement, be aware that there are plenty of known bugs which only happen in the CK (and ye olde CS) after doing certain things... affecting ONLY that session. Restarting the CK and retrying the action (without whatever caused the session-related bug) usually fixes this (apparently as it just did for my Ivarstead).
Have you tried altering the empty Vanilla cells (in an new, blank ESP) with just a basic setup, as I suggested a while back? Try altering the exterior Riften area (in Tamriel), but NOT deleting the Vanilla stuff covering it... ie: navMesh some area inside the empty city (which is behind the non-deleted wall statics), place a door, link it to another door next to the exterior Vanilla door to Riften's interior. Now try bringing followers or placeAtMe some NPCs and test for the 'balcony bug'. If a basic setup in a plain ESP works, you know your issues are related to some other data you changed. It may also be possible that certain areas/cells are somehow tagged as anathema... maybe through regions, quests, or other seemingly non-related aspects.
I'll look into this more - specifically regarding your Open Cities mod... as I need to prove it to myself that this can't be fixed without Ma Beth. I'll try the above and a couple other things, and post back whenever I find something.