Yes — leaving a Discord server does not cancel anything. Your subscription is with Stripe, flatpass is never told that you left, and it keeps billing until you cancel it.
Your subscription lives with Stripe, not with Discord. flatpass is never told that you left a server, so nothing about your billing changes when you go. The next payment is taken on schedule.
The same is true in reverse: being removed or banned from a server does not cancel anything either. Only cancelling the subscription cancels it.
Cancel the subscription itself. You can do it from the server’s flatpass invite page while signed in — you do not need to be back inside the server for that, which matters because /membership is a command that only works from within it. The cancel page has both routes.
Open the server’s invite page while signed in with the same Discord account. The button on your plan puts you back into the server and re-applies your role in one step — the same click covers both, and it takes no second payment because you are still subscribed.
Run /membership in the server and press Manage billing, or use the manage link on the server's invite page. The role stays until the period you've paid for ends.
Run /membership in the server: it re-applies the role on the spot. If it can't, the server's owner has one setting to change and has already been told.
Ask the server owner — they were paid directly and flatpass never holds the money. Cancelling is not a refund: it stops the next payment and returns nothing.