An interesting bug! What happens here is that the factory building has several invisible helper pipe entities that let other pipes visually and logically connect to the factory building. The mod that prevents iron pipes from being placeable on concrete does this by adding an entry to the collision masks of both the concrete and the iron pipes, disallowing both on the same tile, so when you place a concrete tile Factorio automatically deletes any colliding entities on top.
Unfortunately, said mod apparently adds this collision mask entry to any modded pipe too, including Factorissimo2's invisible helper pipes. So by placing concrete, not only did you delete the pipes you connected to the factory building with, but also the helper pipes, and Factorissimo2 was not prepared for its helper entities to go missing. Replacing the factory building works because this regenerates the helper pipes (placing entities via script doesn't check whether this placement is allowed).
I suggest you report to the author of this other mod that it shouldn't add entries to empty collision masks, including a link to this discussion thread. In the meantime, I'll have a look at what I can do on my side.
Thanks for reporting this, by the way, especially after you found a workaround.
