QB64 (Linux) version 2.0.2 running on my Linux-Enabled Chromebook.
Step 1: Made a directory. I called mine "/foo"
Step 2: Wrote a program and saved it in that directory. Mine is PRINT "Hello World", and I saved it as "HW.bas" inside "/foo".
Step 2.1: Compiled and ran the app (sanity check)
Step 3: Went to Chromebook's "Files" app and renamed the "/foo" directory to "/whatever"
Step 4: I had left QB64 running on another display. Set the focus back to it and tried to start the program and got compile errors.
Step 5: Went to QB64's file menu, and clicked "Save As". Left the filename unchanged, but went into "/whatever", and saved (overwriting the file last saved there.)
Step 6: Program still not compiling, scratched my head a bit.
Step 7: Added a couple of spaces after "Hello World"
Step 8: Compiled and ran A-1
So kind of quirky, but not horrible. Then again, I am a stone's throw away from "what am I doing in a room I just stepped into?" (i.e. might forget I've got a file open in a directory while I'm changing the directory name.)
Give the same steps a try with QB64 running on your Windows rig. If Windows is not as graceful-ish as what I've found in the steps above, might I suggest (tongue majorly in cheek; um, the cheek above my neck): you might want to consider selling your soul to Google and switching to Chromebook? Come on over to this side of the Cuckoo's Nest ...