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Good evening and welcome to JA. How many years it has been that your spouse has a Tier 2 dependant visa?
Did she get this visa at the same time as yours?
I understand. In general, applicants can submit a settlement application up to 28 days before they would reach the end of the specified period, but the issue here is that your wife's visa expires before she reaches her 5 years.
There are two way as I see here: 1) Apply for an extension and then vary the application
2) Apply for an extension and once approved apply for ILR, request an IHS refund.
If she will apply straight away for ILR, it may be approved and maybe not. It depends on the caseworker working on the case.
You are most welcome. I wish you a good luck