So long as your previous amplified sample has not been purified then it should have some GDNA so there are 2 approaches

1 use whole genome amplification of the crude pcr (old) product then use 1 set of primers to amplify the new product.

2 Use nested primers for the second amplification. Nested primers give huge amplification and can even amplify single cell dna so if you amplify about 200 bases containing your target then with 2 nested primers amplify the short product. Bear in mind that if you will need to sequence the 100 bp product using pcr prouct and primers then to get 100 bases od good sequence your primers should be 50bp (approx) outside of the final pcr product.

Over amplification producing a smeared pcr product can be a frequent result of nested primers so do not use high cycle numbers of the second amplification

You could use ExoSAP-it reagent to remove the previous primers and unincorporated dNTPs (like you are doing a sequencing clean up).

The "nested primers approach" should work. Even thought the region you really want to know is only 100 base pairs, there is no reason to not try for a bigger amplicon. If you know enough about the genome, why not try for 1000 bp with your 100 in the middle-ish region? That way it's much easier to tell if you got amplification & not just unused primers.

Good luck!

when you say you have run out of dna I have always found that there is dna dried on the walls of the storage tube and in sufficient quantity so that whole genome amplification ( not cheap but very good) will produce huge amounts of dna much of which will contain your sequence and can be diluted greatly to act as template for pcr

Thanks for the great suggestions. Fotunately, the question became moot since the DNA samples were found. But now I have an idea how to proceed should I find myself gDNA-less in the future.

Thanks again!