Billing 69990 with 20922
In CCI under CPT 20922, 69990 is listed in column 2 with note, "misuse of column 2 with column 1". So, yes, this is a CCI edit.
I don't see modifier 59 usage as appropriate here either. Please see CPT 2012, Appendix A, Modifier 59, Distinct Procedural Service, which reads: "Documentation must support a different session, different procedure or surgery, different site or organ system, separate incision/excision, separate lesion, or separate injury...".
Since by its very nature, the operating microscope is always used as an add-on code to a primary procedure, it can't fall into any of the above-named categories. Modifier 59 is much over-used. We need to think through the above reasons before using it with other codes, and not just slap it on because we'd like to get paid.