There was a box that appeared that asked if I wanted to reload from disk
So some other program (editor outside Lazarus), had the same files open. And that other editor had changed them.
Lazarus notices that, and offers to reload them.
Then I can only
guess / One possible scenario / but there could be others, I do not know what was the 2nd application changing your files on the disk:
Assuming the version in Lazarus was up to date, then you did right not to reload them, because whatever was on disk was different on out of date.
If you saved the files from Lazarus, that would have updated the disk versions. But maybe the other program/editor was still open, and replaced the files?
There is another possibility:
If you have symlinks (e.g. ntfs directory mountpoints), and 2 path point to the same physical file, and you open that files from both locations, then you can fool Lazarus to believe that this are 2 diff files, and it will compete with itself.