OK. Using CA glue. It's not terribly difficult - it does help if you have two sorts - a very thin (low viscosity) and a medium thick (medium viscosity) glue. You initially run some of the very thin stuff into ALL the holes, and any suspect areas you see in the wood. It does help if you FIRST put some greaseproof paper at the back of the scales, and don't do what I did first time and that is glue the wood to the kitchen surface. Wow! To be a girl and do that was just so embarrassing.
You will notice that the thin stuff finds its way into the finest of cracks - as you go, if you get any runs on the surface, they can be smoothed while the CA is still wet by rubbing with a finger which is covered in cling film. Once done - clean the glue bottle top and store it in the fridge. It will keep in good condition for a fair time (but you should use it on some more pretty wood anyway). Keeping CA glue (unopened) in the freezer/fridge also extends it's shelf life substantially.
Let that cure overnight inside the house. Then, using the medium viscosity glue - fill in all the holes. The thin glue will line the holes giving the medium glue something to hold on to. You can fill quite big holes with the stuff. It does shrink back as it dries off and cures, so you just let that lot cure (24 hours between applications, sometimes even longer if you poured it in) and then apply the next lot, and the next, and so on until the wood is all filled in and ready to work. It takes time, and you cannot rush it.
Then - as you go with working the knife handle, if you come across any more spots that need doing - you do them just the same. You cannot rush things, and some good advice is to NOT use the CA accelerator to water to help things along - it sometimes causes the CA to cure white. Left quite alone, it cures clear and the treated areas will not be any different from the wood around it when the finish has been applied. So - you can apply the stuff with great gusto and happy abandonment.
One more thing. You can make a little 'dam' or prevent through flow of the CA glue by sticking some masking tape over the bottom (or around the sides) of the hole/piece of wood. Burnish the tape down well with your thumb. Afterwards, this can just be sanded off.
While it can be expensive when used in large quantities (but can also result in good financial reward when you offer a knife in a rarely used, difficult wood), CA glue is brilliant stuff for fixing all kinds of problems in wood, and if the wood is particularly porous, it almost stabilises it throughout.
Hope this helps.
I have found Hot Stuff Red and Orange to be most useful in my workshop - in fact - I am never without both of those, and recently I purchased some 5star CA glue (made in the UK) which is sold as Industrial Strength. This you can apparently use to glue the blades to the liners and the liners to the wood if desired. I would think it will work - after all - that is what holds our airplanes together. Frightening almost.