It sounds like you’re dealing with how aliases work in the game. An alias only fills when the quest is first loaded. If that is saved in your save prior to making changes to that alias, (which includes packages) you will have to start from a NEW save that didn’t have those saved in it for them to work correctly. Believe me, I fought this issue for many more hours than I’d like to admit before I figured out why my stuff wasn’t working like it should. Basically, it’s a major pain in the ass, and makes testing stuff extremely painful. It takes me nearly 40 minutes to slog through my quest to test new stuff now, and that is only going to get longer as I get closer to finishing it.
One thing I’ve been looking at is not using aliases for so many things, and just using regular old properties. I think much of this can be avoided like that.
There is a feature to help with this (check the early MQ quests and Beth left various examples of this ) - My CK isn't open at the moment, though, so my terminolgy will be wrong ... but ...
You can set variables into a quest when it starts - This allows you to have "alternate starts" to your quest ... So sometimes you can skip a part you have already tested and (when combined with a couple of console commands) pick up your quest at the stage you need to test. Still a pain, but better than playing through the same 40 minutes again and again and again ...
I'm pretty sure they work off the "Log Entry" form on the Quest Stages Tab (but like I say, CK not currently open)
(As I put before, Beth did this in the "Helgen" parts of the MQ Quest ... so you can see examples ... )
(you've probably all already seen it, just thought I'd say

)