From what I have heard, if you are going to have a problem with Cipro, you will probably know pretty quickly, within 2 weeks or sooner. I had a friend who went on a trip to Central America and brought some cipro just in case he had any gastrointestinal issues and he had joint pain and tendonitis within a week and stopped. You will not know until you try it yourself. There is no reason to fear taking any medication until you determine it is a problem for you. Many people on this board have taken Cipro for long periods with no problem, some for short periods and had problems and side effects. Same thing with Flagyl. There is also a warning not to take Flagyl with alcohol, yet I have also done this and had no problem.
Warnings are placed on drugs for liability reasons, meaning that the pharmaceutical companies are protecting their own butts as opposed to really caring about what happens to you. They are covering themselves with a disclaimer on the off chance you take cipro and your achilles ruptures on a treadmill. Chances are that will not happen. You should take any warning/disclaimer on any drug seriously but with a grain of salt as well, because the risk is there but is not necessarily a greater than not chance kind of risk.