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After loading my modded (py) save, pipe connections in some places got messed up. Whether i have similar mod set or no mods, the issue still exists. Replacing those pipes fixes them. This is approximately what this area looked like before. The pipes are connected normally. Not sure when this issue became a thing, i know for a fact it worked correctly on 2.0.41, but maybe the issue only happens with certain migrations. I tried loading this save in modded 2.0.51, vanilla 2.0.51, 2.0.47 and 2.0.43, and all have had this issue.

This appears to be related to the Valves 2.0 mod - if I keep valves on 1.2.1 then the issue does not occur.

Weird. The valves in the save are old ones (version <= 1.2.1). But the issue happens even when loading the save without any mods at all. Of course in that case everything is broken, but those pipes shouldn't look like that as they're not even the ones adjacent to removed entities

Yeah, the bug has something to do with the removal of the internal valve entities - whether that be by migration from valves 1.2 -> 2.0, or removing the mod entirely.

It's not the mod's fault, it is simply triggered by the mod's behavior.

Thanks for the report, this has been fixed for 2.0.56.

When a prototype is removed from the game, Factorio will temporarily create a "dummy entity" with the default prototype of that type for the purpose of migrations. In this case, the valves mod removed their internal storage tank, so the game would create a dummy storage-tank entity. Unlike the valve tanks, which were 1x1, the default tank is 3x3 and has different connection positions. Nearby pipes would then connect to this dummy storage tank during the rebuilding of fluidbox connections. Then, when the game would remove this dummy storage tank, the pipes would not find new things to connect with, and so would remain incorrectly disconnected from their actual neighbors.

The fix was to prevent dummy entities from connecting their fluidboxes to anything else in the first place.