Just to add @Caleb Heimsoth comments, look at what options your company might offer for tuition reimbursement.

The rental was out of commission for 6 months and we finally paid out of pocket for repairs to get it back up and running while waiting for insurance to reimburse.

Your initial response seems fine my only additional thought would be allowing them to purchase and install/install their own blinds, reimburse off rent if you're willing.

I even left a message for him saying i'll reimburse him for some of his security deposit if we can agree upon a move out date......I'm really suprised by all this. 

As long as the property is leased, we will reimburse/refinance 75% of the appraised value.

If it's under your landlord policy, not flood insurance, reimbursement of rent during repairs should be fully explained within your policy. 

I was told that I could liquidate a portion of my retirement accounts and then reimburse with a family gift and if it's within 60 days we wouldn't pay a penalty, but that seems a bit sketchy. 

Also if you decide to convert the property to a long-term rental the improvements may be added to your capital basis & depreciated over time.Track Expenses by Account - Helpful for reconciling bank accounts, credit card accounts & expense reimbursements#2 Liabilities / Outstanding Loan BalancesIf you are using outside funding, you will also want to keep track of your outstanding loan balances that you owe for each property.You can do all of this in an Excel spreadsheet by just creating columns for Category, Vendor, & Accounts.

With an owner not willing to accept a reasonable offer, even with all the seller's agent commission being waived, very few options are left for Denver Property Flip to be reimbursed.

I'd seriously consider confronting your old accountant and asking for reimbursement of fees and estimated penalties.