Don't know whether this is an EAP (3296) or 4.x problem, as I've been using
3.x up till now.
Compiling a resource file (i.e. anything that matches compile resource
pattern e.g. "a.xml") in a java module can cause it to be deleted.
Have a minimal test case - made new project with single java module, single
directory for source/output/ipr.
Add "a.xml" and then either compile, rebuild or make - seems to delete if
the file is changed. In fact, just discovered that changing the file and
then ctrl-s caused it to be deleted!
Not affected by choice of output path, no version control, no
clear-output-directory-on-rebuild or anything else that seems to relate.
Doesn't appear to occur for non-resource files.