It's possible to hide some data so that has been already indexed with the delete command, this makes it no longer searchable.
It isn't reversible (and off by default), so measure twice, cut once.
You can force reindexing by a couple of different methods. You could reindex everything using a
splunk clean eventdata on your forwarders. You could force reindexing of specific files by copying them to $SPLUNK_HOME/var/log/splunk, though the paths will be a bit different. You can tell splunk to index a particular file regardless of the duplication logic with the oneshot input method: splunk help add oneshot
Lastly, a bit dirty, you could get somewhat sneaky and defeat splunk's redundancy checking. If you modify the first 256 bytes of your logfiles, eg by inserting a single character of whitespace at the start of them, it will reindex those files, assuming they are totally new.