So as usual I ended up planting some mandrake (putting 13 on the ground at a time to 39, on a swamp, with a hero with no units), but this time I ended up leaving the hero on the tile for over a day. So when I move him off the tile finally, there's no mandrake growing there, nor any on the ground. Tried waiting until the server restarted in case the graphics didn't update or something, but it's still a normal swamp; Located at the NE of my two public (flag) markers.

You didn't plant it correctly (btw it doesn't have to be a hero with no units, you can plant with anything that has an inventory, any hero or even machinery).
The growing starts when you move away from the cell. What happened is it just stayed on the ground, and whatever is thrown down disappears in 1-2 days (usually after the downtime). We Admins don't know what really happens - either greedy orcs steal everything left unattended or the planet likes to keep itself clean.
Anyway if it's a bad loss (the only mandrake you had) we can generously provide you with another set.

Nah, I have some more. Just a bit annoyed because I was going to expand to a third swamp as soon as this cycle was over. ^^;

I have had a problem with my 1st attempt at harvesting Mandrake.

I sent a hero with no troops (but wearing artefacts, including boots) to collect the mandrake and he was not given the option of taking it.
I sent him back WITH an army and he was given the option of taking all 52 roots BUT when I tried to take them it only gave 39 and there were still 13 on the ground which I could not pick up. I tried sending the hero back to get them but they were gone

Could Admin please tell me exactly how to collect them? I have more ready for harvesting at the moment & would not like to lose my 2nd crop.

Thank you for your help.

I just send a hero with an army to trample the mandrake, then only pick up 13 of it (leaving 39 behind) and move off the square. This harvests and replants in the most efficient way.

Yes that's exactly what needs to be done.
If you need all the crops you'd better send a wagon.
Most of the guys have a hero with 1-2 dragoons that harvest crops and make new plantations, since they have the most of AP.

That's because heroes are not allowed to carry more than 39 units of mandrake.
As the guys mentioned above, you usually collect the crops (13 units) and leave the remaining 39 units for another 5-day season.

Thank You All

It now makes perfect sence to me