Any idea what New Yorks ADU laws are?

It's a far more complicated issue than REP in general.

Zoning should not be too much of an issues, but uses may alter parking requirements. 

Just wondering what the implications are of changing a single member LLC to a multiple member LLC as far as current depreciation, basis, carry forward losses and any other issues. 

There's a ton of information available on these forums if you're ever unsure about anything, take a look around, chances are another person has encountered the same issues and share their experiences on here.

The Management Company is recommending at this point, because there is a dispute, to send some kind of bill showing that this work was done and if not, it would be best to issue a refund.

I-if it's "big expense", I get ahead of this issue by whipping out a receipt book (you can buy one at any store like Target, Wal-Mart, Staples, Office Depot, etc) and jot down the work that was performed, materials, hours, amount of people, other expenses, etc.

There's no benefit to anyone if they can’t rent the rooms, so your interests are their interests, and they're looking out for you - they actually recommended I back out of the first house I put an offer on due to foundation issues that they weren’t comfortable with.

If so, would this still cause issue with the S-Corp tax rules?

As you may be aware they do not issue a refund.How is your duplex working out?