Issue is reported here:
henkelmax/pipez#50

Pretty sure this is on their end. No idea how pipez works (so if you are supposed to have to manually reconfigure a pipe connection if a side becomes invalid and then valid again there is nothing that can be done as everything on both ends would be functioning as intended), but as far as I am aware the general/common handling of when a tile goes from not exposing a capability to exposing it now is by firing a neighbor update notification to the blocks so that it can recheck it (as unfortunately unlike when going from a valid connection to no valid connection there is no lazy optional for us to invalidate as when there is no capability initially we return an empty lazy optional). For good measure we call both onNeighborChange and neighborChanged in case a mod is listening to only one of the two things. From the sounds of it they may not be listening/overriding either of these methods on their blocks?

Edit: My suspicion is if this is the case and you connect a pipez pipe to any factory of Mekanism machine and just cycle through the side config until it is set to NONE and then cycle it back to a side that can be connected the connection to the machine will not automatically be reinstated either given the handling is the same there as for our multiblocks for how we notify neighbors that they potentially should be rechecking if we have a capability or not.