In order to get sound advice on your situation, you need to consult with an attorney and allow that attorney to review the lease and any photos you have. There is other information missing from your post that will be needed: How long was the tenancy? Did you complete a move-in inspection report? What about a move-out inspection report? Were you present for the post-tenancy inspection? Was anyone else with you (someone who could testify on your behalf)? Who gave a 45 day notice to vacate? Was this termination of the lease done prior to the natural expiration of the term? Do you have any proof of your cleaning of the floors (i.e., a witness or photos/video)?
The Virginia Residential Landlord Tenant Act does provide you with some protection here in that the landlord can only retain the security deposit as allowed under the lease and applicable law (the re-capture fee certainly appears suspect (even more so if crossed out and initialed)). This is a situation in which you may be entitled to recover your legal fees, so you should consider a consultation with an attorney to determine the best course of action.
Beyond that, I am sorry I cannot provide you with a more specific answer, but I have not reviewed your lease, have not seen any photos of the condition of the premises, and do not know the timing involved (i.e., did the landlord comply with notice in a timely manner).
DISCLAIMER: The information you obtain at this site is not, and is not intended to be, legal advice. You should consult an attorney for advice regarding your individual situation. While I invite you to contact me and welcome your calls, letters, and electronic mail, contacting me does not create an attorney-client relationship. Please do not send any confidential information to me until such time as an attorney-client relationship has been established (as by signing a written legal services agreement or by entering an appearance in court on your behalf). Any response is intended solely to give you limited, general information on the issue presented. Michael J. Carmody is licensed to practice law in Virginia, the District of Columbia, Maryland, and Tennessee.