You could try filling the honeycomb with a good quality silicone sealant. I've done this on minor sole holes with success, but you have to give it plenty of time to dry, I'd say at least 48 hours.
Also, if the holes are very big, fill them with sealant in stages, rather than all at once, and give plenty of time to dry before doing the next stage.
Patience is required, but I know what it's like to love a pair of boots which need a bit of help!
Sue, April 2008