There is a constant IndexAfterStartup that is used in the microflow SUB_AfterStartup to update the index with the new objects to index. This seems to me that it shoould not delete the index and rebuild them, but worth to have a look at maybe?
The after startup microflow looks for the current list of specializations of the GlobalSearch.SearchableObject entity, will remove objects that are no longer a specialization and objects that are new ones will be added.
Maybe the list of GlobalSearch.SearchableObjectCache objects is not correct anymore?
Just some ideas I’d look into hope this helps you further.
Were you able to find a solution to this issue? We are facing the same problem in the Mendix cloud. Locally no issues.