We have experienced a similar case in which an Expired Instance would be added to the License Master but could not perform any searches.
The thing that we found out is that since the Expired Instance did not joined the Master, it started to use its Free License option without us realizing. After the Free License expired it blocked all Saved and Adhoc Searches, at this point we tried to make it join our License Master successfully but could not still perform any search.
The fastest solution that worked for us was to ask for a Reset License on Splunk Support Portal stating that we hadnt notice the violations ultil it was too late. They answered the same day with the Reset Key that you can upload to the Expired Instance directly (You must first separate this instance from your Master License Server and then apply the Reset Key to the Expired Instance directly; after it has cleared you can make it join the License Master again)
The other option was to migrate the data from the indexes ($SPLUNK_HOME/var/lib/splunk) and also selectively transfer the configurations ($SPLUNK_HOME/etc) to a freshly installed Splunk Instance, and then join it to the License Master.
Hope it helps
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