I have had no problems with re-PCR, but I haven¥t tried the same method
as you. I used low-melting point agarose gels, glass-milk, or
freeze-squeze metods to get the DNA out of the gel. Which method depents
on the size of the band. More than 500 bp, glassmilk is quicker. Less
than 500 bp; - glassmilk won¥t always let the DNA go, so I prefer
freeze-squeze (modified by diluting the agarose pieces in 0.3 M NaAc pH
7.0, before freezing).