There is nothing in principle "wrong" with merging two separate programs running on two different sets of hardware (but sharing the same FPGA code). However, unless you are extraordinarily careful about how you develop your code, and take great precautions to keep the various codes "segretated", "mistakes will be made".
You might consider separating your code into three segments: one segment that is common and shared by both routines, which you'd place in a "shared Library", and two separate Projects for the two PXIs (which, I presume, do either different things with different hardware, or the same things with different hardware using different top-level code).
At some point, the two Projects will "naturally" separate -- one system will require slightly different requirements (possibly related to its different hardware), or the differences in the PXI hardware will suggest "pushing" the more capable hardware to "do more". In such cases, allowing the two different routines to "naturally diverge" will be easier with two separate Projects.
In either case, don't do anything until you put this Project (or Projects) under some form of a Version Control System (such as Subversion or Git).
Bob Schor
