I have an MXD that points at a single point file with about 80 records stored in a FGDB that I had published to a folder in ArcGIS Online and subsequently overwrote without problems. I did this once a month for 6 months without issues. I tried to overwrite it the other day and got the packaging succeeded but publishing failed 99999 error. The logs showed nothing, that generic code isn't helpful, if you're reading this far down you know the drill. I was trying anything I could to get it to publish, I had moved it to the root and that didn't work. I deleted the service and the SD, didn't work. I renamed the service when I re-published, didn't work. I renamed the MXD to be completely different than any service name and published with that name, didn't work. Even had Fiddler running. I finally got the crazy idea to run my MXD through the MXD Doctor. After I did that, it worked, it published. The MXD was 1.3 MB before (bloated by re-saving), and after the "treatment" it was 66 KB. I don't know if the planets aligned perfectly or there was divine intervention, or our network magically uncluttered itself to allow outbound data, but it worked. I am going to test this the next time I have this error with this and reply back. I can't with any certainty say this solves this issue, but it may be worth trying. Just my two pennies, hopefully it's helpful. Again, I had deleted the service and SD so this was a straight publish to the root, not an overwrite of the old service in the folder. Oh yea, I was publishing from within ArcGIS Desktop 10.3.1, Advanced License, 64bit PC, 8GB RAM, and 1GB network speed, and Symantec Endpoint AV software I can't disable.
