Thanks Scott and Rick:
This is not a big problem -- everything works fine in FPD26 Extended, which is where I usually work. No corrupted files, and nothing needs to be fixed. Scott planted a seed in my brain, though: maybe I've been transporting something "bad" in my project from computer to computer for my tests. So, we started over and conducted JERRY'S SCIENCE FAIR PROJECT:
I loaded FPD26 STANDARD, started in a clean directory, created 125 brand new PRG files (named FILE0001.PRG through FILE0125.PRG), with a single line of code (? "Say this"

in each file. Then I made a MAIN.PRG with "DO FILE0001", "DO FILE0002", etc., adding files to MAIN.PRG one at a time, having the Project Manager REBUILD PROJECT each time. With each BUILD, I checked to see if I could REMOVE FILE0001 from the project, save the project with ctrl+w, then reload the project with MODIFY PROJECT MAIN. After adding FILE0112 to the project, I could no longer really REMOVE any files. The REMOVEd file disappeared from the PROJECT MANAGER window, but after saving and reloading the project, the REMOVEd file reappeared. The magic number of project files seems to be 112 (not 106 as reported earlier). I also checked this out using FPD2.5a with the same result. Note that this is not a complete failure after #112 -- the Project Manager still compiles large (120+) APPs and EXEs that work perfectly. Scott may have had this problem with his 120+ file project and never realized it unless he tried to REMOVE a file or change a Screen Set Code Option.
The bottom line is, this is just a "heads up" in case your Project Manager starts behaving strangely some day. Maybe you'll remember this thread and you'll know how to work around this little FoxPro anomaly. Thank to all.
Jerry