Can confirm this is also the case for me.
(Also playing latest commit of the repo)

Same problem. I move far away from a crops and then get back. The crops are disappear. With this bug farming is impossible.

Been poking at this. It does save a plant progress value which gets loaded again.

The Planter doesn't seem to exist yet when the Plantable is deserialized.
PlantableMetadataProcessor will always see growingPlant as null, and do nothing with the stored progress variable.

I tried to force it to recreate the plant, but have not yet been successful.

Edit:
plantable.currentPlanter is null after deserialization, likely relevant.

Edit 2:
The items contained in the planter are in seed form, and decomposing, after re-loading the area. This implies that the planter doesn't invoke its Spawn() function, as I believe that triggers the cycle that would replace those seeds with plants, disable decomposition, and create the growingPlant/GrownPlant as required. Not 100% on anything, still wrapping my head around a lot of stuff. Just tinkering and sharing my observations so far.

Edit 3:
I missed that this is already being worked on in a much more elegant fashion over here: #2137
Mentioning in case anyone else ends up here.

It seems like using the fastgrow command after joining will bring the plants in the growbed back to life.
You can then turn it off again after that and they seem to work fine (until you disconnect again).