This has been a long standing issue for us, and I thought there was already an idea for this but cannot find one, so here goes: Please adjust the rest endpoints of a service to NOT be index based. In other words https://.../mapserver/0 should instead use a name of a layer or perhaps a unique layer name (https://.../mapserver/fences or fencesGUID from the properties of the layer, so that sorting the layers in the mxd does not adjust the rest endpoint when it is republished. Although you've worked around it with popups and static ids a bit, it is not the best solution for other access requests.
