My wife has an UK ILR (Indefinite Leave to Remain) and while a naturalized US Citizen, has been returning to the UK every two years (in fact every year or more frequently). So as far as we know, her ILR is still currently valid.
If they have been letting her in using her ILR, then she could still claim to have it. It may have been cancelled without her realizing it though if she was allowed in as a visitor and they did not recognize her as a permanent resident. Such things have happened to the dismay and later surprise of people before. The biggest problem is that the UK has now introduced exit controls. If your wife is just visiting for a few brief periods of time over a period of years, the UK is fully within its right to say she is no longer resident, much less a permanent resident. And this would all come to light in your son's ILR application.
You should know that the UK ILR has absolutely zero value in the rest of the EU, except perhaps to expedite Schengen visitor visas.