Indoor Air Quality/wet filters
We are renting a condo in FL and found a wet filter upon arrival. We changed it and it didn't take long before it was wet too. I called the landlord and she tracked down her maintenance guy. When he arrived he said it was ok. He said that we had the temp too cold in here. What!!! We told him that we were afraid of possibility of mold in there and he told us to spray Lysol in the vents. Do you believe that!!! Our landlord swears by this guy and says he does good work. I am ready to call my own technician. We change the filter every couple weeks cause I am afraid of the damp filter making us sick. Why is it so hard to find good honest people that know what they are doing??
Your problem with the A/C system could be simple to fix, like a fan speed adjustment and duct balancing. Or it could be more serious, like the system is sized improperly for your space and the cooling loads, or the ducts require better insulation. You definitely need a competent technician to diagnose and fix the problem. It is not normal to have all that condensation or moisture in the air stream and on the filter.
I would recommend that you leave the filter out and get someone there soon to do a proper work up. Unless your place is really dusty, then leaving the filter out for a short while won't hurt. The primary purpose of the filter is to protect the air handling unit, fan, and ducts from dust build up. A secondary purpose is to improve your air quality. But right now your wet filter could be a bio-media for microbes, so why leave it in?
Also be aware that if you are getting wetness on the filter you may be getting wetness on the interior of the ducts. These surfaces can support microbial growth as well. All in all, you need to get the system fixed and keep wetness out of the air stream.
And forget the Lysol, or most other chemical products. You need to be very careful about what you add to your indoor air.
The US EPA has a good article on duct cleaning (including ozone and biocides) that you may find helpful: http://www.epa.gov/iaq/pubs/airduct.html
Best of luck, and let me know if you have any more questions.