Technically speaking, "harvester" in this context is just "a zone" (say, "West Harvester") with one small entity (Lab). You mine this small entity. Putting down the small entity anywhere on the overworld map causes the mod's code to paste the "West Harvester" on that small entity. Whatever you put the "West Harvester" on, is now where the "West Harvester" originally was. So it's basically a "zone swap".
When starting a new game and unlocking the "West Harvester", it's a blank zone where you can't put any miners on (since miners need resources under them for them to be valid). So the first thing you do (or well, can do), is pick up that small entity and drop it right on the ore patch. Then put the miners on. Now, when you pick up the small entity again, it'll take all the entities (not the ores) with it back into base (The original "West Harvester" location). This allows you to now put the small entity anywhere - even without ores - and the miners will come with it.
So what happens with mining drones? I don't know as I didn't test. But the depot will disappear, leaving any miners behind that weren't on the platform (i.e. ore patch too big or you just decide to put the "West Harvester" next to an ore patch instead of on top of it). So my guess is that this is what the problem is. Perhaps the Depots also don't activate properly when, say, ores "suddenly" appear on the area the depot would harvest from where there previously was none. So yeah, that manual scan.
When your whole factory warps to another planet, the old surface also gets destroyed (With a few exceptions such as "Home Planet"), potential cause for more issues?
