9.05.600B Deleting epicor directory

During the installation of the 9.05.600B patch file I see a batch file executed. It is called something like "clean up apps.bat" It looks like this batch file deletes some things like replication server instances. In my case it deleted everything in my E:\Epicor directory except for 68 files in the oe102a directory, and it doesn't touch the oe102a_wrk directory. It did however erase my 803.4 folders, 10.1b, and 10.1c folders completely. I have reinstalled my oe 10.2a instance and applied the sp3 and hf 11 files, however my conmgr file does not have any of the epicor specific info in it. As a result I have no db's or appservers appearing in my progress explorer tool. Support has me reinstalling the 9.05.600 SP to see if it will execute the scripts to create the requires files (I have my doubts). Has anybody seen this at all, and what are my options for getting back up?