If you pay the money into the registry that means that you are allowed to assert your defenses to the eviction action.
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You can be evicted if the judge finds that you did not pay all of the money due.
Since you paid the money that you believed was due, you should be entitled to
a hearing (at which you can testify to these facts).
Make sure to get copies of proof that you paid (receipts from the LL, canceled checks,
redacted bank statements, stubs of money orders, etc.) and make sure to
be able to explain in detail what the offsets were and have receipts for the money
you spent on replacements and repairs from any vendors that you used or parts you
bought from stores.
If I understand the question correctly, you are just dealing with your landlord’s 3-Day Notices, which means that an eviction suit has not yet been filed against you. You will know if an eviction lawsuit has been filed against you because you must be served with the court documents personally.
If there is no lawsuit yet, you do not have to worry about putting any money into the registry. You must wait until you are sued. After you have been served with the court documents, you have 5 days (excluding Saturday, Sunday and holidays) to file an Answer and deposit rent due into the registry. If your defense is that you paid the rent in full, you do not have to put the rent money into the court registry either. But remember, for all other defenses, you must put the money into the court registry.
Your only other option is to file a Motion to Determine Rent which means you will have to set a hearing with the judge to figure out how much, if any, rent you owe. This option does not require you to put money into the registry, but you must always file an Answer within 5 days of being served with the court documents along with this motion.
This is a general answer based on a very general question. This answer does not create an attorney-client relationship. That said, I hope this helps.