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The pathability issue appears to be unrelated to the temperature. The temperature is reset to the standard subterranian ambient temperature, which should be safe in most circumstances. This behavior appears to be shared by the tiletypes and liquids commands without issue.
The issue here appears to be that when the tool is set to magma, the liquid_type of the tile is set to magma, which appears to have a lingering affect. By going over an affected area, removing with the tool set to water, the walkability groups appear to be regenerated correctly. This leads me to believe that setting the liquid_type to water when the level is zero should prevent these symptoms.
This issue did seem to affect the liquids command as well, when using the commands m and 0 to remove magma.
In addition to the issue of tiles being placed into different walkability groups, it may be desirable to set df.global.world.reindex_pathability to enforce the regeneration of the walkability groups following any modifications to liquid levels.
In particular, removing magma on an empty tile (no magma) will set the tile to magma temp
From Reddit: https://www.reddit.com/r/dwarffortress/s/M1AYoBv1l6
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