Like several others, this change screwed up my simple "move drones to the right" cloning setup. I experimented with several ways to distribute drones including some complicated setups with gates triggering iron pipes; most of these solutions were pretty space intensive.
The solution I came up with uses one router to solve the problem simply and is very compact:
Original princess/drone pair in leftmost apiary, princesses to convert in the others. Wooden pipes with autarchic gates to extract bees/items on queen death.
Apiarist pipes on the back set to move princess back into the apiaries along the red line and 'anything' on the yellow line. Diamond back on the back of the router is set with one drone of the type you are attempting to clone along the red line into the router. Mismatched drones and items go down the black line to storage/genepool/void.
Router configuration is a snap, don't even need any upgrades:
Default insert mode, set to insert into slot 1 (the bottom breeding slot) of the apiaries. The router will evenly distribute the target drones in the bottom breeding slot of all apiaries in the line.
Once all the princesses are cloned, the lever is to stop the router so you can collect them before they breed again.