Having the SD file is only required when publishing from ArcMap. If you must publish from ArcMap, i suggest republishing the sd file and feature layer. You can enable delete protection on the sd file to prevent it from being deleted accidentally. You can overwrite feature services from SD files through the Rest API or using ArcGIS Pro without having an uploaded SD file.
Here is a sample script that is publishing from an FGDB, but the same concept applies:
