Posting in the name of @johanneskoester:

If those jobs are finished, Snakemake will not rerun them, because their output files are there. When creating a report, Snakemake will however warn that their metadata is missing.

If jobs still run when starting the main snakemake again, it will complain that their results are incomplete, but it currently has no way to see that they are actually still running. It would however be possible to extend individual executor plugins in that direction.