Good question - I have discussed it with my Spanish wife and whilst we are not tax experts or solicitors we think this: The notary you use when you complete on the sale has to by law retain 3% of the sale price if the seller is a non resident. This is paid to government as a retention until any taxes due are calculated etc.
However given your mother has been living here but unfortunately forgot to renew her residencia it might be best to ask someone in authority (doctor, bank manager etc) to vouch for her so that she might be able to obtain the new certificate backdated to the card expiry date (if this is possible) then she can complete as a fully fledged resident!
Or, perhaps the notary might accept she has lived here as a resident by the utility bills etc. and take pity on her and let it go through as a residents sale.
Hope this helps - post again when you make some progress!