I have confirmed now that the app is no longer replicating the lookup files up to the indexer through bundle replication. However, when I use the Use Case pages, I'm seeing the error above in the Data Check panel. When I click on the Open in Search link, I see that it is using a REST call to determine if the lookup is available. However, the REST call is going against the search peers (which no longer have the replicated copy) and not against the local Splunk instance.
I traced the configurations back to the JSON files in appserver/static/components/data/samplesSearches and saw where that REST command was coded in the test values for each of the use cases. I appended "splunk_server=local" to each of the REST calls. After restarting Splunk, the Data Check panels were now reporting correctly.