After a warning, that I might be hacked, I changed my password. Now, after catching pokies all morning, they are gone....anybody know how to fix this?

Google account or pokemon account? If it's google i'm sure there's a way out of it, I mean I don't think anyone in this world is sadistic enough to hack someone's google account to transfer pokemon over stealing credit card info.

If it's a pokemon account though, I'm not sure what will happen

The new pokemon or all your pokemon? You don't make that clear in your "title".

Put your phone in a bag of rice

How did you change your password?

did you follow the link provided in the e-mail?
if so, NEVER do that!
Hopefully you have unique passwords to all of your accounts. If not, Stop everything.
the least of your issues are your pokemon.
1) change your e-mail password first.
2) change accounts involving money. then work down from there.