There is no problem keeping your bacterial genomic DNA by boiling method for furhter investigation. I usually storage them for a good time at -70 or -80 and have afterwards a good PCR result!
if you add to your DNA Tris-HC pH 7.8-8.5 at a final concentration of 10 mM and EDTA at a finale concentration of 1 mM, your DNA will be stable for years or decades at -20°C, whereas if you keep at 4°C it will be stable for several months, and at room temperature for several days.