I have feature services published to an internal portal that over time lose feature layers for some reason, and thus break the web maps using those feature services. What causes a feature layer, that has no changes to it at all get dropped or lost from a feature service? There were no changes made to the feature service, or the web map consuming the feature service, and the web map worked for several months, then all of a sudden stopped working, and in investigating I found that one of the feature services had missing feature layers that had been there and working before. No database changes were made to the schema, only data uploads were performed. I see this after the feature service has been published and sitting in the portal for a few weeks to a few months.
I have the same problem on our high available portal. I publish new feature to an existing feature service by overwriting it. After a few times, the service suddenly is not available in the map. My Content shows the feature service. The only thing that helps, is to delete the feature service and publish it as new one.
I have had issues in the past with overwriting feature services, so now I just delete them altogether and republish (which of course breaks any web maps that consume those feature services, adding more publishing work). My case is different in that after publishing the feature service, no changes are made to the database, feature classes, or feature service at all, but still after a time I see feature layers that were originally in the feature service disappear, and I have no idea why or how to prevent this.