When a monitoring is setup with ignoreOlderThan attribute, it'll exclude all the files which were last modified earlier than the set value. Those excluded files are not included back automatically when they are actually updated. To have Splunk re-evaluate the monitoring file list, you need to get the Splunk (forwarder) instance restarted. If you've a script/utility using which you can re-start all forwarders, do that. Otherwise, you can make some changes to existing app or create a new dummy apps and assign to all fwd with restartSplunkd=true.
I have a very similar issue, but we use heavy forwarder and there are thousands of files that have already been indexed (<7days old) and are stored in the same directory; if I change the ignoreOlderThan attribute to say 90 days, will already processed files be re-indexed again?