Why not just start out with new substrate?
Depending on what you're after, you can get a 50-60lb bag of natural pea gravel for ~$3 at Lowes
You could move/re-home the babies now I'd think. I've had molly fry get sucked up into hang-on-back filters and survive no problem. What solution
oh tanks petluver.
Most fish you do not have to acclimate, that's what plop and drop means.