This happened to me temporarily when I uploaded a new file and overwrote the old one with the same name. Changes in the IDE didn't seem to stick when editing the new file.
Another time I have observed this is when copy/pasting a large amount of text (big section of code) into a file in the IDE. Never did wait long enough to find out if it was just a processing delay.
I solved the problem by using the IDE buttons to dele all the files I wanted to replace and re-uploaded them.
I will add this note to the github page also.