http://bugs.winehq.org/show_bug.cgi?id=10324
--- Comment #10 from Vitaliy Margolen vitaliy@kievinfo.com 2007-11-07 14:20:16 --- (In reply to comment #8) Well it does not destroy it, it makes some important files owned by root and 644 permission: $ls -la ~/.wine total 488 drwxr-xr-x 2 vitaliy vitaliy 168 2007-10-07 09:33 dosdevices drwxr-xr-x 4 vitaliy vitaliy 168 2007-09-19 23:12 drive_c -rw-r--r-- 1 root root 437211 2007-11-07 13:17 system.reg -rw-r--r-- 1 root root 2392 2007-11-07 13:17 userdef.reg -rw-r--r-- 1 root root 53649 2007-11-07 13:17 user.reg
That's what breaks. Unless you have some other suggestions about these files Wine really should quit before doing any permanent harm.