Ah, I see the problem. The mod doesn't touch Bastila. The only thing it edits in that module is the script that endlessly spawns mooks, adding various new Dark Jedi to the spawn list. But the module has scripts with + and other characters in their filenames, and the old versions of TSLPatcher fail to save them in ERFs/MODs they edits. K1CP uses an unreleased fixed version of TSLPatcher that doesn't have this problem.
You can just take the exe from the K1CP folder and use that with my mod instead to reinstall it and it should be fine. I'll upload a fixed version of my mod that includes that exe. Thanks for bringing it to my attention.