I have taken cipro (and other antibiotics in rotation) continuously for over 20 years. The most important thing you can do is rotating off cipro and on to another antibiotic periodically. I haven't had any long term side effects or issues, but if the drug is not used properly and rotated, then you can have issues with it and/or it can lose its effectiveness.
Cipro and flagyl work well in tandem because they are from different antibiotic families and work on different bacteria. Cipro should never be rotated directly to levacquin which is from the same fluoroquilone antibiotic family. I generally favor xifaxin after a cipro rotation because cipro is broad spectrum antibiotic which kills many bacteria while xifaxin is not systemically absorbed and allows skin and other bacteria to regenerate. This will protect your body from opportunistic yeast and fungal infections that could otherwise develop from taking cipro at too high a dosage or for too long a period of time.
By the way I have no thyroid gland due to thyroid cancer and take 175 mcg synthroid and there is no problem there. The only issue with diabetes is that some of the symptoms of diabetes (numbness and tingling in the extremities) mimic some reported possible cipro side effects. If you experience this you will not know which is causing it unless you stop the cipro.