Instant Search Indexing Issue

I have my parcels service indexed on our HTML5 viewer. It was working great but then I did an update to the parcels service (this will be a monthly occurence), Essentials then started to re-index the service (expected), however, when it did that, it disabled our ability to search for anything within the Parcels service (parcel ID, address, owner) until I went into rest manager and disabled the index. 

This is highly inconvenient, is this a known issue or is there a different work around available?