I'm no expert, so all disclaimers apply. If an expert happens to show up, please feel free to discard any erroneous or useless info that I may have provided.
In spite of all that, here's what I do...
On something like a knife sheath or gun holster, I tool/stamp first, then mould (carefully) in order to minimize damage to the design. Also, I don't soak the leather for more than a few (maybe 10) seconds. Lately, I don't even do that. I'll just run it under hot tap water and let it rest a few minutes. The re-dampening itself has little effect on the tooling. It's also a good idea to layout your stamping/tooling so that it's outside the areas you'll be boning/moulding if possible. Otherwise, it's gonna get squished.