Can I use a hardening wood filler over softer wood putty on a walnut island?
It would be much better to remove a soft filler and fill any holes from the bottom up with a hard filler, otherwise you risk the hard filler being undermined by the soft material underneath — sort of like building a house on loose foundations.
It might just be possible for a hard filler 'cap' to work its way loose in time, after a few cycles of expansion and contraction. I have certainly had shallow fills that didn't bond well to the depression they were in1 be dislodged during subsequent sanding.
From the Comments:
I doubt I can get it totally clean
It's not absolutely necessary to get every trace of the original filler out of the holes (and practically, this can be virtually impossible) but do aim for mostly clean.
If the previous filler was any of the usual kinds of wood putties they tend to have a fairly dry and crumbly consistency, so it may not be difficult to remove most of it once you get at it with a pick, awl or other sharp tool!
Once the bulk of it is gone brush out as much of the debris as you can using stiff brushes, even some fine wire brushes if available (brass or stainless steel are reasonably easy to get these days and very cheap).
And if necessary wash the interior with a solvent of some kind if you want to take the cleaning one step further.
If the previous filler was a wax cleaning with a solvent would be of particular importance since wax is a 'universal resist' and basically nothing will stick to it (other than more wax). You can use mineral spirits, VM&P naphtha or paint thinner if you have any of the three. Don't skimp on the solvent and use plenty of paper towels so you aren't just spreading around the dissolved wax but are actually soaking it up and removing it.
Would you recommend glue and saw dust versus shellac? I thought shellac may work better for this application.
Glue and wood dust would be preferable to shellac and wood dust for anything but the shallowest defects. In addition to shellac filler material of this kind2 taking longer to dry for a deeper hole (because the alcohol has to work its way out of the interior before it can evaporate) it will just plain be weaker.
If you go with the DIY filler you're familiar with based on a PVA wood glue it can be coloured a tad darker if you wish with a dab of acrylic paint. Even though the glue & dust fill will naturally be darker anyway (approximating the colour of end grain once the finish goes on) defects in wood do tend to be quite dark, often nearly black, so fills can look best if a good bit darker than the surrounding wood.
Epoxy as the binder material is also an option but a little more difficult to get flush with the surface because it's so hard once cured.
1 Either because I didn't prep the surface properly or didn't provide any undercuts for the filler to grip.
2 Commercial shellac fillers (AKA burn-in sticks) are a different thing entirely, very hard and tough, because there's no solvent in them.