That's interesting, I kind of expected something to come up & try & hit those immigrants that came before the current nonsense. My wife came here August 2002 & was granted ILR a year after arrival, if there was a requirement to obtain Citizenship it was never communicated to me. She has worked so many years in that time, paid her NI & Tax so this BRP thing is surprising but not unexpected. My wife's employer does things 'by the books' and its never been communicated to me that she needs this.
I need a Google session to find out more about this. You would have thought that your wife's passports would be proof enough to detail her time in & out of the UK. If this was me I don't know how I could prove that my wife was in the UK when we had young children & she wasn't working - that's a real tough one as I pay all the bills - wow.
I'm sure it will all be sorted but you can certainly do without it.