This is a story and question. I'll state my question/issue first.

After the 11.2.4SP1, I had to manually copy some files from a temporary server I installed 11.2.4MU1 onto my production box because zman wouldn't run without throwing Java.class errors. When I ran ZDC, it showed a lot of files not present, so that's when I copied the files and everything was A-OK.

I also see issues regarding %ZENworksHOME%\conf files not being accessible even though they are present, and some files in \share\tomcat

This leads me to last night

Last night I started the upgrade, then went to do some other tasks. At some point the server was restarted. I didn't think that was a good sign. Anyway, ZENworks Loader wouldn't start, so I ran the ZDC for 11.3. I see the same issue with \conf and \share\tomcat. This time, some of the \share\tomcat WERE actually missing.

I tried running the install twice more. Same thing. I install 11.3 on a temporary machine, copied \share\tomcat from temporary to new. I fixed permissions on \conf again, and \share\tomcat. I set them to Everyone along with SYSTEM and Administrators. I was missing a bunch of \install\downloads\MSI as well, so copied them from a temporary machine.

I ran through the install one last time. Everything completed without error. Now, everything is up and running, but when running ZDC again, the \conf files are showing as MISSING. Again.

Also, the Audit database is shows several hundred tables missing and the ZEN DATABASE is showing to NC_PruningLog tables errors.

I'm not sure what functionality I'm missing. Clients are updating to 11.3. The ZCC seems intact and Patch Management starting Updating Cache when told.

I'd say the first failed upgrade was caused by something outside of the upgrade, but what is up with all the permissions issues and missing files?