Using stabilized holly and the other wood helps. Holly is a wood with an open grain that does tend to pick up stains.
Here are some tips for working holly and other white woods:
Sanding sealer will greatly reduce the issue. Apply it once the scabbard is rough shaped. Repeat as you sand down if needed.
Sand in strokes parallel to the holly not across it.
Use gentle pressure in sanding and wipe away the sanding swarf frequently.
A vacuum hose positioned close to the sanding pulls the swarf away as it forms. They sell an articulated vacuum arm that can be positioned to put the nozzle right where you want it.
Using a tack cloth helps.
Blow off the dust regularly with an air hose and plenty of pressure.
Alternate idea - consider another white material, like white G-10.
Just my thoughts, but are you sure you want that white stripe on your dirk scabbard? I have seen a lot of dirks, made a few, and made a LOT of skein dubhs, but that just sounds a bit odd looking.
Here is my dress skein dubh in black and white mammoth with silver fittings:
