A great bookkeeper will keep your books up to date monthly/weekly.

Alternatively, you could explore options like cash-out refinancing to access equity while keeping low interest rates and established cash flow, or a 1031 exchange to defer capital gains taxes and reinvest proceeds into a similar property.

I'm also new to the Series LLC, and keep coming across that most folks are not familiar with this format because it's not offered in all states, only about 16 states offer this format.I have a Series LLC in Ohio, and at one point started one in Alabama. 

He is keeping his properties here while living out there.

You will need to keep a time log. 2.

I am thinking that 12 months worth of pet rent will equal about the same as a deposit, and with pet rent, I would keep it no matter if there is damage or not, but with a deposit, I would only be able to keep it if there is damage.

I understand you tried that and it was rejected but I think you just need to keep putting offers out there. 

If a partnership turns into a single member LLC due to a partner leaving, a new EIN is required but how would a business still keep the branding of their original name if creating an EIN requires a different name?

If you sold it, what would you do with that money and how much income would that generate compared to keeping the house with the added costs of buying out your partners? 

Our current focus is working on 1-4 unit fix and flips, but eventually work towards being able to refinance properties and keep and cash flow them.My question is  tailored on the the way I should structure our relationship for the legal and tax base purposes.Should I secure the deals under my business and pay my partner out of my business operating account?