Landlord Question and Answer Forum

Our tenant is moving out end of September and gave her final rent payment on the first of the month, however, the amount was for less because she took off the security deposit. I didn't know what to do at the time but later decided to email her and explain that was not allowed according to the lease agreement and am mailing her check back for replacement of a new payment for the full amount. She finally agreed but it is 3 days late now. What should I do??? She also decided to make her final payment via check although the lease addendum specifically indicates payment through an online app, which she has done throughout up until the last rent payment.