If it's a pony bottle, I would leave it pressurized and ready to use at all times, so no risk of flooding the 1st stage.
Not to nitpick, but in the interests of full discussion, if my pony is only 13 CF, because I think that's all I need at 100' for 1 min at double my usual RMV to problem solve, then a normal ascent, safety stop and surface, then I can't afford ANY accidental purges. Yes, you can say, "carry a bigger pony", but I don't for rec diving.
That means turning the set off after pressurization is a reasonable course of action, and thus flooding can be a concern (which is why I stay pressurized, but use an inline shutoff).