I have been using PerioProtect trays for close to two years, but I was told in the maintenance stage I no longer need the antibiotics, so I no longer use the tetracycline. I was also told that since the antibiotics are used in a subclinical dosage, your body won't develop a resistance and it isn't harmful. Also, I remember being told something like, "if you taste it, you waste it" --- meaning, you don't swallow it, you merely use it topically. I hope this helps. I have really been helped by this system and have told many of my friends they need it.
I am not sure that an antibiotic should be used for that length of time. I would consult a periodontist if your gums are that bad, otherwise I don't see the necessity for this treatment for this length of time.