You send your landlord the 1099, not the other way around.
Include the receipts & labor for the work you did in the total amount paid to him in the "non-employee compensation" area of Box 7 and the total rent you paid in the "rent" area in Box 1.
He can only send a 1099 to you if HE paid YOU so if you got one it was probably in error.
Couple of things, you don`t say what year you are dealing with.
How much was the value of the rent. He gave you the 1099 so he could take a deduction for the value of the rent.
And yes, without records you are pretty close to screwed. That is undeclared income and will be subject to taxes and penalties. You may wish to consult a local accountant to be sure. Depending on where you live you could be afoul of State laws on the subject as well. Call to see if there is a JK Lasser office near you or someone else who specializes in tax negotiations.
The audit is because if you "forgot" about this, what else did you "forget" about from their point of view. If your bank records match your tax return you will be in pretty good shape. If you "forgot" more income you could be in for a full run. Plan on paying up, but they are pretty good about settling with you nowadays. Not as good as the Clinton years, but pretty good. They also take credit cards so you may be able to rack up some air miles while you are getting out of trouble.
Now the situation becomes a little more clear. In your original post it sounded as if you were paying rent and did a few repairs to your own place in exchange for part of the rent you would normally pay.
If he gives you an apartment in exchange for being a maintenance man, then he has every right to send you a 1099 or W-2 because housing is a form of wages and has a monetary value. By placing you in an apartment he`s giving up the rent he would normally collect for it.
It`s up to you to provide proof of repairs so you can take the deductions on your taxes. For the most part, it`s your labor that will have the most value and not the parts.
Did you sign an agreement with the landlord where he puts a price on your labor? If you did, then calculate the resulting value and send him a 1099 accordingly.
Alot of people barter "off the books". The government expects you to report the full value of the barter ON the books. Very few people actually do this but you should document the exchange for your own protection.
The effects of not keeping good records [barter or otherwise] can ultimately end up in a dilemma such as yours. Now the burden of proof is on you.
At this point, all I can suggest is go over your bank and credit card statements and try to get copies of the receipts for your past purchases.
I wish you luck on your audit.