I would like to add to this.
I recently upgraded to High Sierra and was having no issues with xojo, saving or any other file system stuff. I recently changed the name of the directory where all of my xojo projects were saved. I saved in xojo after I had moved them out from under xojo control not really sure what I was expecting to happen. In other mac apps like numbers it keeps a reference to where that file is saved and no matter where you move the file, it still saves in the same place. I did a bunch of work then xojo crashed. Usually its, not a huge deal, I Just reopen xojo and carry on where I left off. Much to my sadness, about a week of hard work was gone.
I looked through all my backups, (dropbox, timemachine and github) nowhere could I find my missing code and not once did I get an error or any hint that it wasn't truly saving. I deleted the entire folder and resaved as a xojo project (for src control) Checked the files and confirmed that it was saving. I continued on and then I closed and reopened the project only to find it had not been saving again.
I did some experimentation and found that adding or removing large parts of a "xojo project" that save in their own file (like classes and modules) will write to disk. However, small changes like lines of code and methods will not write to disk.
Can anyone confirm this is happening?