Is there a modifier that can be added on to CPT codes to show we performed the service even though they are bundled charges or Medicare doesn't pay for them? For example 97140 billed to BCBS or 99202 billed to Medicare. Is the GY modifier for all insurance companies or just Medicare?
I suggest you check out chapter 5.6 of the 2017 ChiroCode DeskBook which is all about modifiers. Also, the ChiroCode Online Coding Library includes a tool called the "NCCI Edit Validator" which allows you to dump in codes and find out which ones need a modifier and which ones can't be billed together at all.
For any service you submit on a claim to Medicare that is not 98940, 98941, or 98942, you should add modifier GY, which tells CMS to deny the service. GY means "statutorily excluded". It can be helpful if you need a denial to submit the charges to a secondary for beneficiaries who have another insurance plan. For example, an E/M might be billed as 99202-25-GY.
The GY is only for CMS. The 25, which would be used for all payers, is necessary to let them know that the E/M is significant and separately identifiable from a CMT service billed that same day. Similarly, the 59 modifier (or newer X modifiers that may be used in its place), identify a service that is distinct from a CMT, but it is for codes that are not E/M. Per the NCCI edits, this only applies to 97124, 97140, and 97112 when billed with CMT. There are other combinations that might need a modifier though, and that is why the "NCCI Edit Validator" in the ChiroCode Online Library is so helpful.