If the deed is silent, presumably the HOA docs say something completely different about garages... and since you should have been provided both prior to settlement, this is stuff for you and your attorney to figure out.

So the question would be will the buyer's bank allow an assignment fee on the CD/Settlement Statement?

As far as you know, there may have been other collateral securing this loan or the bank entered into a deed in lieu or some other kind of discounted payoff, reached a settlement with the guarantors, etc.

Pending litigation could have been decided with final judgment entered; perhaps litigation initiated involving the property, lis pendens recorded; federal tax lien could have been recorded... lots of things can happen before settlement.

First you get excited , after settlement you get buyers remorse , when the furnace dies a month after settlement you feel pissed off .  

We are borrowing 250k over 3 monthsWe just received their estimated settlement statement which seems to carry a significant amount of junk fees:Amount requested                                   250,000.00type                                                             2nd trust deedterms:                                                         no pre payment penalties after 3 monthsrate                                                             10%Points 1,75                                                4,375.00lender Underwriting                                795.00lender Admin                                            700.00lawyer fee                                                   1,000.00Escrow Fees                                                450.00title co Property Inspection Fee              75.00Notary Fee                                                  175.00Electronic Recording Fees to title co       20.00Lender Refinance Policy to Title co         1,032.00Endorsement - estimate to Title co         125.00Recording Fees to Title co                         75.00Deed of Trust Recording to title co         150.00total junk fees                                             $4597It is the first time we use a hard money lender, but to me 50% of these fees are avoidable and should be negociatedCould you guys give me your opinion about these terms and what are the fees you'd pay and wouldn't?

I will not own the properties until after closing/settlement, and will be in the middle of the month when this is complete.

You can't make money at the settlement table unless you are a realtor. 

Application is made for a lien abatement for the amount the liens exceed the purchase price... and once approved settlement can proceed.

Either the seller needs to pay the lien at settlement (if there is a lender involved... see below) or the buyer needs to factor in taking care of the lien immediately.