Thanks for the help guys. Here's what I'm doing:
1) I'm creating a copy of TestQuest01
2) I'm loading up Rosethorn Hall into that cell because I want a duplicate of it, but this could be where the problems are coming from. Instead of editing the Rosethorn Hall in Skingrad, I simply want a copy of it to edit and use somewhere else.
3) In the Data section, I have Oblivion.esm, Knights.esp, and DLCShiveringIsles.esp selected, but my mod as my active file.
Does anything seem wrong? You should know I'm getting a bunch of error messages upon start-up, like "errors were encountered during InitItem for reference."
What assertion error do you get ? If you get it everytime it is a problem you should solve in priority. Sometimes it is innocent sometimes it is serious.
For the multiple warnings and the crashes it is because you used knights.esp in another .esp and duplicated things you should not. Whenever I try to duplicate cells I created in a mod to another mod the CS crashes on save, due to incorrect references no longer existing ( esp use dierent masters) but it is normal.
In your case, you probably get a 0 kb .esp and a .tes file. You just need to rename the .tes file, to .esp, load it again in the CS, save it without changes and clean it with TESedit. And keep in mind you need to create new REFID for each object imported, delete the old one and use the newly created one or change manually the refID. Tedious but if it is an important cell it is worth the time
eg : if your .esp is 03xxxxx and the object you duplicated refers to 02xxxxx you can get some weird issues, like a NPC used as a static object, and more often if you load several .esm or .esp and he reference is found but not of the correct type. In TESedit you can chose the REFID and apply the correct one, or even create one to replace the "error could not be resolved" but you have no way to see easily if the found ref is of the right type. CS is unforgiving for this and throws thousands of warnings and most often crashes. If it loads, it will crash when you open the cell in the render window and of course when you enter the cell in game.
Why can't I use the Knights.esp? I'm not setting it as my active file, I just wanted to use objects from that DLC. Does that still cause problems?
Also the first time I load up the CS prior to creating the mod, I don't have any active file selected, then when I first save, save it as a .esp and set that as the active file next time, is that correct?