I feel you… I guess it has to do with the fact that there is no synchronization, is a one way process. Since Engine Prime has no way to know what was converted to the old Engine format on the drive, it just work all files again in a one way direction. So if you hot cue some files directly on the controller they will get overwritten.
I don’t use Engine Prime to export my files to the drive. I export the files directly from Finder/Explorer or with VDJ. Then I drag them to Engine Prime, this way the files are already on the drive.
Inside each music folder it gets created a hidden folder that contains all the analisis of the files with its hot cue. So the next time I have to use Engine Prime and I don’t want those analisis files to get overwritten what I do is I change the name of all the hidden folders.
Next time I have to export with Engine Prime I open the new analisis folder created by EP, arrange them by date, copy the new ones to the old folder that I change the name temporarily, delete the new created analisis folder and rename back the original hidden folder back to its original name.
Is a hassle I now, but that is the way I get around so it doesn’t overwritte the hot cues I created on the controller.
I also tried once, just before exporting with EP, selecting all the analisis files on the drive and making them Read-Only then when finished exporting with EP then I go back and change its properties to its original property state, but that was a long time ago and I don’t remember the outcome of the laboratory I did, as a matter fact I will try again to see.