Glad to hear you find LiveIndex useful!
What I would do (as a workaround) is to temporarily replace the other character style with some text styling (e.g. underline, or a special swatch or something). Then you can apply the page-number style to all the numbers and run LiveIndex.
When you’ve finished with LiveIndex, replace the underline or swatch with your required character style again.
Does that make sense? Let me know if I’ve misunderstood something.