Greetings and thank you for your great mod !
So....
The vanilla rocket-control-unit(rcu) recipe gets converted correctly but later on Bob overwrites all ingredients.(Leaving me with stacked output from unstacked input). The offender is "bobrevamp_ ... \prototypes\rocket-parts-updates.lua"
Feeling like a complete failure, trying to solve this for a few hours now. Finally gave up and just manually edited the correct ingredients into the recipe.
Maybe you could handle this in a proper way, in case there are more (vanilla!) recipes that get only their ingredients messed up.
PS: tried setting bobrevamp as prerequisite mod for yours but that obviously didn't fix anything^^