1) Running the command on multiple surfaces in quick succession.
Shouldn't really make a difference other than increasing lag. There's no maintained state involved that having multiple going at once would impact; each chunk ends up handled the same way no matter what. Unless one usage of the command interrupts another when it's doing the chunk request loop, but I wouldn't have thought they would do that. (Also, that part runs very fast.)
2) Trimming the surface and re scanning it.
This, on the other hand... did you trim the surface before or after running the command? Because if you trim a surface after the new resources are generated, it's expected that they won't come back (and mentioned in the mod description). Trimming the surface before running the command should not have any negative impact.
Is there any danger in re-running the command? If so I can load my safety save after blueprinting my progress and run the commands again with a larger gap between them.
Nothing it does carries between saves, so if your safety save is before running it then it should work just fine. If it's after running it, then it won't let you run it again.