We have been replicating/syncing data from an SDE database for a while now and I've just started to notice that every few replica syncs to utility databases (file GDB's -- all created with 10.3) the queries to from those databases have slowed down dramatically. For instance, a simple LIKE query on a single attribute of points goes from < 2 seconds to nearly 10 seconds. This is really noticeable through ArcGIS Server map services. I can re-create the replica and the queries are back to normal (< 2 seconds). The SDE gets a nightly cleaning/compressing/re-indexing.
Does anyone have any insights as to what might be the cause? Is there some post-sync cleanup to the file GDB's that can be done? It seems like the indexes are getting out of whack.
Thanks in advanced for any help.