(United States) How do we protect separate money within a charity?

I work for a medium sized nonprofit in a paid role.

We have 3 softball teams that play in a local league. Our softball group does not receive any money from our agency, but we do house our money in an account with the agency and use their accounting system for invoicing/purchasing. We collect dues and do our own fundraising like a club within the organization. (We even have elected representatives.)

Under new management our funds have now been restricted, and there have even been threats to absorb them into the general fund. I get that economic times are tough, but this was never agency money. We fundraised 100% of it ourselves.

What will it take for us to retain our independent access to our funds in this situation? We have benefitted from nonprofit status because we're a subgroup of a 501c3. If we take our money to a bank (instead of leaving it with the agency) can we keep our nonprofit status? or will we have to file as a separate 501c3?

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