I notice the warning when you overwrite the project file. The problem you describe is real, but there is a simple way to avoid it
create project-tempxxx
write update to project-tempxxx
close project-tempxxx
delete project
rename project-tempxxx to project
With this technique the worst case is that the rename does not occur.
Of course since windows caches writes you are not really save unless you insert a flush to force the temp file to disk.
