This probably is what it says it is - there are files and/or directories missing from the disk.
Have a look in the Admin -> System info page to see what your "Jira Home" directory is, if you don't already know, then log into the server and check that in that directory, there is a "caches" directory. If there is not, then create one for it.
You should also check the ownership of Jira home and all its subdirectories and files - they should belong to the account that Jira runs as. (Actually, you don't really need to check all of them, on Unix-like systems, you can just issue the fix command of "chown -R jira:jira" assuming the account is called jira)
Once you have made sure the right directory is there and owned by the right user, restart Jira and try a full re-index (not background).
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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