A couple of ideas here:
Make flasks available for purchase, just like the others.
As you reach certain level milestones, give a 10-15 seconds reduction in time to regenerate a new flag.
Make the regeneration run concurrently from the time it was used. Currently, you use a flag when it’s generated, but the clock for generation on the next one starts when you finish with that one. In essence, if you start with 0 flags, it could take 9 hours to have 3 shots. This would allow you at least have another shot an hour later or so. The current timing is way over the top!!