After emerging a tool that basicly only untars a file a remerge of the same tool will almost completely remove all files during the clean phase. (this happened when I did a emerge -e world as instructed for updating the CFLAGS for xen, for several such packeges) How about just touching ALL files in the install image before qmerging files?
this is a dupe but i cant seem to find the original ... there's a bug open already that covers portage removing files/dirs during the autoclean step even though the new ebuild just installed it
Dupe of Bug 54669 (which is dupe of Bug 16162)... *** This bug has been marked as a duplicate of 16162 ***