Nothing about deleting the files is fixing anything, it will just rebuild the index so anything that didn't get indexed before because of the errors will be indexed. If the error is still happening it won't rebuild the index, thats why I said to back up the files.
If that path for lucene is not correct it will still error when it tries to build the index. Since it indexes on a background thread you won't see any UI error but it will log errors in the log.
I would make sure you aren't missing any of the indexbuilderconfig files. They should be located at /Setup/ProviderConfig/indexbuilders
There are 8 files there, all 1K each in size. Make sure they exist. This location has moved since previous versions, it used to be under /Setup/indexbuilderconfig folder.
Hope it helps,