So here's the story. One night my brother went in and fixed a bunch of scene and quest issues we's been having. He saved and created a backup that night.
The next morning I continue; testing the quest and scene to see what changes were made. Everything is okay.
I make another backup (to be safe) and began working on one of our cells (cluttering and that mess...) and after about three minutes decide to load my backup instead of manually deleting what I had. (I know I shouldn't have done it.)
Long story short - I don't know exactly what happened - once I was done working for the day the scene changes that had been made were gone, but all my changes were there. I must have loaded the wrong backup. I then proceed to open my brother's backup and copy my updated cell into the .esp where the scene/quest changes were made. After my splicing everything seems to work okay, however there is a notable issue. After visiting my copied cell (coc MOD1HallsofInsecurity) I cannot return to a specific point in Whiterun using the coc command (coc WhiterunPlainsDistrict02.) I am not sure if this is the result of my tinkering or what, however, the problem only persist once per load (That is while visiting my cell and using the coc command to Whiterun the command will execute properly the first time. Punching in the command a second time successfully loads the Whiterun cell and everything is working again.
Any help or insight would be greatly appreciated.
Additional Information:
Process for copying the cell
Opened Creation Kit
Loaded Skyrim.esm and Update.esm
Loaded MOD1Q.esp (the duplicated cell's original .esp) and Test.esp (a temporary .esp used to store the cell) with Test.esp being the active file.
* I did this because a direct move results in duplicates of all cells as the original and target plugins are both iterations of the same file (one was a backup)
Duplicated MOD1HallsofInsecurity (duplicated cell) and renamed to MOD1TempSaved to Test.esp
Loaded Test.esp as active file
Rendered Cell MOD1Temp to clarify cell transfer.
*No Problems
Loaded MOD1QAlt.esp (duplicated cell's destination) and Test.esp with Mod1QAlt.esp as the active file
Deleted MOD1HallsofInsecurity
Re-Loaded MOD1QAlt.esp (duplicated cell's destination) and Test.esp with Mod1QAlt.esp as the active file
Renamed MOD1QTemp to MOD1HallsofInsecurity
Saved to MOD1QAlt.esp
Loaded MOD1Q.esp as active file
Rendered Cell MOD1HallsofInsecurity to clarify cell transfer.
Saved to MOD1QAlt.esp
Renamed .esp files
*"MOD1Q.esp" to "MOD1QMain.esp" and "MOD1Alt.esp" to "MOD1Q.esp" to match .bsa
Tested*No problems except what is listed above.