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[PatrikLundell]

I've muddied a fair number of stone tiles underground (10 levels down) and have been growing on these underground plots successfully for years, but suddenly in year 7 I noticed that nothing was growing (month 7 day 18, I think), and checked why: All of the plots suddenly display the message "No seeds available for this location", despite me having a fair number of underground seeds of all kinds but Dimple Cups, and even then they should be visible, just displayed in red. I've checked that the environment is still displayed as dark/underground (how the surface would get down there without crawling along my convoluted tunnels would be a mystery anyway). This condition remains as autumn turned into winter.
The biome on the surface above the area is arctic sea, and just as an experiment early on I muddied some rock the level below the surface, exposed it to the sunlight, tiled over the opening, and created a farm plot that, as expected, displayed the message I see now.

Any idea of what's happened (probably as summer turned into autumn) and why (This isn't a soy bean plantation on burnt rain forest, after all)?

Edit: I've created a bunch of new plots in the 3:rd cavern under the same biome, and they can be used normally (but I get a long hauling distance).

[Bouchart]

Possible shenanigans with bags.  If you just made a bunch of bags, they'll be used by dwarves filling them with loose seeds all over the place.  It's the same problem other containers have- if the containers are in use for a job the contents can't be used by dwarves.

[PatrikLundell]

No. My replacement plots work just fine while the original ones are still useless. Bags would just cause cancellation spam, but since the seeds actually exist in the ledger they'd show up as possible to plant (in white, even). I don't even get red text on my afflicted plots.

[Bouchart]

Are you sure you didn't accidentally set the farm plots to fallow?  Is the farm plot accessible?

The only other thing I can think of is if somehow the biome changed, which I don't believe is possible, but I'm not certain on it.

[PatrikLundell]

I can't have changed each of the 30 or so farm plots at the same time (I made each tile its own plot as I created them as the bucket brigade dropped water), and that was the first thing I checked, but again, even if fallow, the list of legal options should contain the season's crops. The farm plots are located in my open area workshop where each workshop is surrounded by space, and the argument above holds on accessibility issues even so.

I haven't heard of a biome change, and certainly not of an underground biome that does not support farming when muddied. The seeds in the seed stockpile in the tile beside one of the farm plots have a temperature of 8 degrees Celsius, and so is above freezing.

[Pancakes]

I had this problem once, and the only way I was able to continue farming in the same area was to either:

a) Select fallow for a year or so

or

b) deconstruct and re-build the plots

Unfortunately, those are the only solutions I am aware of for this problem

[PatrikLundell]

Removing the plots also removed the mud, so reconstructing would require remuddying. I won't be able to pursue the issue due to a fatal crash, though.

[Sirbug]

I think opening a single tile of a plot ruins it.
This might happen if you build plots in soil and through roots, then somehow tree gets destroyed - cut or collapce.

[PatrikLundell]

This was deep underground on muddied stone and all the plots were single tile (below an ocean beside a glacier, no no surface trees at all).

[kelewan]

This was deep underground on muddied stone and all the plots were single tile (below an ocean beside a glacier, no no surface trees at all).

mud is removed by some actions like smothing stone.

[PatrikLundell]

While the area was smoothed, the rock beneath the plots was not, so the smoothing skipped the plots. The mud disappeared as the plots were removed (there is mud on the remaining plots, as I only removed 3 of them).