The ArcGIS 10.3 GeoEvent Extension Patch 1 for Server, now available on the Esri Support site at the link below, includes a fix which I expect will address the issue you are describing.
http://support.esri.com/en/downloads/patches-servicepacks/view/productid/66/metaid/2181
Specifically, we discovered that GeoEvent Services, published in the 10.3 release, which included filters with spatial conditions (INSIDE, WITHIN, CROSSES, etc.) caused the GeoEvent Services to disappear when either the GeoEvent product's service was restarted, or the GIS Server was rebooted. The upcoming 10.3.1 release will also address the issues addressed in Patch 1 above.
- RJ