Security Deposit Issue and Ongoing Leases

[David Triplo]

I closed on my first property a few weeks ago and have somewhat run into a snag and would like some advice how to handle the situation.  I now own a 3 flat in a good area in Chicago.  The main large unit is rented out by a youth organization and was informed that the organization paid the rent.  After closing I found out they only paid half and the 4 tenants split the remaining portion of rent.  This organization has been in the building for a few years now and have a great relationship with the building and previous owner.  The previous owner didn't handle the security deposit properly and now the tenants believe the amount is $200 less than what they paid.  They signed the estoppel statement, received money for consideration to release me from his error in handling the security deposit, and signed an security deposit receipt from me all stating the lower amount. Would you consider paying them just to keep the peace?  I'm considering splitting the difference.  The total lease is $3600.  They just inquired and haven't been demanding or anything.  

Also on a separate note, there can be turnover mid lease between people.  The organization takes care of finding new tenants and there's always a waitlist for a room.  What documentation would you have when they turnover?  The organization isn't on the lease despite paying half the rent and curious if I should be adding them when they renew the lease?  The organization does vet out the tenants so it shouldn't be likely I have issues with a potential new tenant.  From a security deposit standpoint, I was thinking the new tenant would pay the tenant moving out and there would be no transaction with me.  I'd appreciate all the advice!