I would give the snake back and ask for a refund. Mites are UNACCEPTABLE as it is EASY to rid a collection of mites vs dealing with them for YEARS.
If that's not an option, read on...
Soaking the animal in water that's not too deep is generally a good idea to rid the animal of a good number of mites on their body, and hiding in their scales. Don't make the water too deep as you don't want the boa to have to continually swim in it. Water should be about the same temp as the boa - make sure it stays that way. Soaking for a good 30 minutes to an hour is a good idea. WHILE SOAKING THE BOA...
Completely clean the enclosure and everything in it. Dry it all off. Then, spray provent-a-mite or Black Knight II as instructed on the cage. Others swear by other products but I don't have any direct experience with them. One is a product that wal-mart sells under the... "equate" label, I believe. Also spray the substrate which should be paper towels if the snake isn't too big and paper towels are unrealistic. Paper towels makes identifying more mites easy.
Get the snake out of the soaking tub and dry it off well. You should see lots of little dead mites in the water. Once the snake is dry and the cage is dry (from spraying the mite spray and allowing it to air out), place the snake back in the cage.
Retreat per the instructions on the can of mite spray at least twice.
Don't spray the snake directly. Seriously. Don't do it. I don't care what anyone else says... don't do it.
If you have other animals, I would spray around their enclosure so that all entry points have a coating of the mite spray so if any mites try to get in, they can't.
Quarantine is a must! Also, don't handle the boa with mites, and then go handle your other boas. You'll probably have mites on you! I recommend a minimum of 3 months quarantine for a healthy animal. For an animal with mites, a year would be a good idea (hence the recommendation to send it back) maybe longer.
As for long-term effects... as long as the mites aren't carrying any diseases they picked up from other reptiles, there shouldn't be a long-term effect as long as you rid the boa of the mites.
jb
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What's written above is purely my opinion. In fact, MOST of what you read on the internet is someone's opinion. Don't take it too seriously 
Jonathan Brady
DeviantConstrictors.com
Deviant Constrictors picturetrail
