I'm sorry to hear that your girl is having these problems.
Dogs with floppy ears are prone to all sorts of problems with their ears. It's very possible that these cysts are the result of pores that are blocked by ear wax or debris on the skin. So the first step would be to keep her ears cleaned very regularly - every day. I would wash her ear flaps with an antibacterial soap (put cotton balls in her ear canal to avoid getting soap and water into the ear). Then you can use cotton swabs and Q-tips to clean out the nooks and crannies of the ear with an ear cleaning solution.
The smell that you mention indicates infection, which is consistent with a cyst. This could also be the result of an infection that simply isn't going away. It's possible that after the pocket bursts, the area drains, but the infection remains, and the same damaged pore may be simply "re-filling" as the infection re-develops. This is very possible and in some cases, the only way to completely break the cycle is to have the damaged area of skin removed surgically.
When one of these cysts forms again, I would try to drain them sooner rather than later. You can do this by applying a warm compress (like a warm washcloth) for about ten minutes, as this will soften the skin and bring the infection to the surface. You can then lance the area with a disinfected needle and drain as much of the contents as possible. When you're done, you can apply some antibiotic cream (not ointment, as this can clog pores and create more problems). This should help promote healing. If the area appears to be re-filling with pus, you can repeat the draining process, which may be necessary several times.
Another option would be to try her on some topical steroids (to help with inflammation) and oral antibiotics (to help with the infection). Both would have to be prescribed by your vet, but it is a non-surgical option that may be effective in your girl's case.
Is there ever blood? If so, she may be dealing with pockets of blood, which can be triggered by head shaking and ear infections.
Here's a bit more on aural hematomas, in case you think this could be a problem for your girl:
I hope your girl is feeling better soon! Don't hesitate to let me know if you have any additional questions!
***Please ACCEPT if my answer was helpful!***