He explained the prior tenant hung a picture there, drove a nail threw the wall, dented a pipe. 

They ones that need new roofs, have broken pipes, no heat source, or have water damage.

In January...pipes froze in a 6” fire sprinkler system in a mixed use property.....10k the owner agrees to do the work and give me 90 days.

If your CPA doesn't have viable solutions for you, then make sure you exhaust your idea with more professionals as you may outgrow your CPA's "traditional" knowledge.

The house is listed for just under $600K, but it has significant damage due to broken pipes.

I can pre-authorize an amount and if the expense is below that, the vendor can do the repairs without talking to me live4) Urgent maintenance issues - say a pipe breaks, or tenant is locked out.

Is there a chance the water was on and all the pipes froze and then flooded the place?

You're going to want to follow the following general rule of thumb:- 0.5 mile radius- same zip code- Sold in last 3 months- Same unit count- Same bed/bath count- Same square footage(this is not fully exhaustive but they're the big ticket items)If the appraiser selects comps that are closer matches to the above than the comps you want to use, you're going to have a tough chance arguing for the usage of your comps over theirs. 

Will see how it's shapes up for due to some other constraints like angle of stairs coming down and movement of drain pipes.

I can pre-authorize an amount and if the expense is below that, the vendor can do the repairs without talking to me live4) Urgent maintenance issues - say a pipe breaks, or tenant is locked out.