Prometheus
It seems to me that you do not understand how PAK files work. R:TW looks into those ZIP-like files for certain files. If the files are not present in the PAK then it will in the normal directories.

So if an item is normally located inside a PAK with the following path:
ITEMS\

Then if you delete the pack then R:TW will look for it in:
R:TW - INSTALLATION FOLDER\DATA\ITEMS\

So while you deleted the PAK you didn't place the files/folders into the data directory -> R:TW can't find the files -> CTD.