Compile errors on HPC

I have one related question:
If one runs the precompile trick while existing runs are on-going, does it affect the existing runs?

I have multiple branches (with variant behaviours) of the same module, and the simulations take hours to days to run. I would like to know how best to switch branches, precompile, run job arrays on the current branch, all without impacting the already running jobs.

Many thanks!