Please correct me if I misunderstood the facts you are conveying.
There is a property which was owned or at least purchased by Owner A. He had a loan with Pag-Ibig and the property was mortgaged. Or was the property being paid for in installments, where title to the property would be transferred to the buyer only upon full payment?
In 2003, your mother decided to purchase Owner A's rights over the property, probably by giving a downpayment and assuming the responsibility of payment of the monthly amortizations, but no formal transfer of the loan was made.
The property was under possession of a lessee who moved out after you told him that you are now the owner. The lessee said that he was renting from Owner B.
After the lessee left, you occupied the property, and Owner B filed a case against your mother based on forcible entry.
Now, the Court of Appeals has already ruled on your appeal on behalf of the plaintiff, and you have been ordered to vacate the premises.
Are you sure it was the Court of Appeals which issued the judgment you received, or it was the appeal to the Regional Trial Court after the MTC decided the case originally?
An ejectment case is not supposed to resolve the issue of ownership, only who has the better right between the parties to possess the property. If ownership is raised, the court may pass upon this question, but only to decide on the right of possession.
You have raised ownership as a defense, but still the case was decided against you. Apparently, the courts have decided that, based on the evidence submitted, it is Owner B who has the better right to possess the property.
Owner B claims that he bought the property from Owner A, although Owner A denies this. Was Owner B able to show any document to show that the property was sold to him? What document did you have to show that the property was sold by Owner A to your mom?
I'm afraid I cannot agree that your mother is an innocent purchaser for value because of the ff:
1) the property was not in the possession of the Owner A at the time you bought the property. it was in the possession of a lessee of Owner B. it was incumbent upon you to investigate this matter and determine from the lessee why he was there.
2) the property does not seem to be fully owned by Owner A in the first place at the time that you bought it, if you are saying that NHMFC will issue a title in his name.
3) it does not seem that NHMFC agreed that the rights to the property will be transferred to your mother's name because you are still paying in the name of the first owner. if this was purely voluntary on your part for convenience, I do not believe this was a wise way to purchase the property.
I am not saying that Owner B automatically has better right of possession, but if he has a notarized deed of transfer of rights signed by Owner A, then that may have been the basis for the court's judgment. it would then appear that Owner A sold his rights over the property to Owner B before Owner A sold his rights to you.
the legal principle that may be followed in double sale is that: first in time has better right. this is the extent of what I can say given that I am not able to review the entire record of the case.
regarding default, you mentioned that you were unable to appear after 5 days. this gives me the idea that your mother was not able to file an answer to the ejectment complaint and she was declared in default and the case was decided based purely on the evidence presented by the plaintiff.
your lawyer, whether the old or a new one, would be best in position to say how to prepare a Motion for Reconsideration. I must say, however, that it is very difficult given that the case has already been reviewed by the MTC, RTC and now the CA. good luck!