I published a mosaic data set as a map server using my arcgis server 10.5.
the tile generation process is finished but not all the tiles were generated.
I tried the tool "Manage map server cache tiles" several times, using "recreate all.." and also "recreate empty.." and nothing works.
it is stuck on 99.9% and there are about 14,000 tiles missing.
Are the tiles actually missing (i.e. you can see the holes in the cache), or are you just basing this on the 99.9% and the number of tiles in the "report tile cache status" window?
I've found that that window is not always accurate. (There have been a few threads discussion this) Sometimes renaming or moving the Status.gdb (in you cache folder for the service) and letting it rebuild (i.e. use the "report tile cache status" again) can help, but not always.
But if you do have a spot that you know the tiles are missing (and you know the resource for he area is available, you could cache just that extent to see if that works. (also, check the logs for any errors)