I can't give any advice when it comes to upgrading to a new tank as I've never done so. I would make sure that any new water matches in terms of salinity, temperature, and other parameters.
However, I do know that the beneficial bacteria does not live in the water column. The bacteria is present on surfaces; rock, sand, etc.
I don't know what you're doing in terms of the substrate but I know you would need to be careful if moving sand. It would depend a lot on how long the tank containing the old sand was set up prior, how deep, cleaning practice, etc. because it would harbor nutrients that could cause issues. I think its common practice to use new sand. That would deplete some of your beneficial bacteria, though I'd say you could seed with some of your old sand to help.
Also, depending on your stock, amount of live rock, and any other surfaces that would harbor bacteria that probably wouldn't be a big deal.
I'm sure someone with more experience with saltwater and upgrading a tank will come along and explain better.