Chyos's response:
"this really is a strange bug... all buildings have been removed but without any materials gained in the process... If I didn't know better I would say save edit has been used to remove everything... and that of course would mean that the resources which are created as a side effect wouldn't exist...
But who knows... maybe something else happened and all gathered resources were turned off without starting the next step...
I will add another exception check that will check if all buildings are removed and in that case even if there are no materials allow the building process. that should fix the problem in future versions. that will be applied in 0.6.1.0
tell him to put this into the data folder of the game. that should fix it (I attached the file here)
this has part of the changes made to the orc spawn in it... that shouldn't be triggered though since it's not tested and also involves changes to other maps that are not included in this one... so he better shouldn't go and talk to guards to kill orcs himself"
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I bolded that last bit because it seemed important.
The fix worked, thanks to both you and Chyos for the attention.