If you're using Linux, Git Bash on Windows, or any other viable option that allows you to run bash scripts, you may use this to cleanup your source files:
*** Remember to backup your files first!!! ***
B4X:
#!/bin/bash
#Project Cleanup Script
# - Replaces all tabs with 4 spaces
# - Removes all trailing white space
sed -i 's/\t/ /g' *.b4a
sed -i 's/\s*$//g' *.b4a
sed -i 's/\t/ /g' *.bas
sed -i 's/\s*$//g' *.bas
Nice.
There is also a sed version for windows, so we can do this in .bat, and remove the dependency from bash.
Also, I would prefer to not do inline replacement, as you said, just do the backup in this same script. i.e. sed "regex" infile > outfile && mv infile infile.old && mv outfile infile
...and if you really want to make sure it works, also run a b4a commandline compile, and check it all compiles, and then autocommit!