If you pound 1/8" wood dowels into the holes (assuming they used #6 screws), you can start over again and drill new holes, including holes that overlap with the ones already drilled. If the soles are leather, they will also rot less quickly if unused holes are filled.
Can't you order insoles from the boot maker?
To make new insoles, carefully trace the old ones on cheap insoles from the dollar store or drug store that are a little too wide, and cut the new ones to match the tracings. Then add tape or adhesive foam underneath to give them the same thickness and top contour (if the same is what you want). Should take about 5 minutes. If the fit isn't close enough to stay in, add a glue or double sided tape underneath that doesn't stick too well, so you can take them out and redo them if the new ones go bad too.
Why did the old ones wore out so much faster than the boots?