Amplicon as Template in PCR for TOPO TA Cloning - (Dec/01/2012 )

I don't think you can get shorter fragments (like 100 bp) if you cut 505 bp from gel. I rePCRd gel-purified products several times, usually for sequencing, and it was fine in all cases. Cloning is more sensitive to residual short fragments than sequencing, that's true, but you can easily select the right clones by colony PCR even before you grow them in minipreps.