Family permit + old and new passport

[microlab]

I am UK national living in EU.My wife is non EU,has residency stamp in her old passpor(visa expires in 7 months).She has a new passport where there is no residence stamp.She usually carry both.
We just applied for Family permit,stating that we would like to visit UK for a few days.Would that be problem?
I found out that by EU law these stamps/visas are not transferable.We would have to apply again and simply I did not want to waste 4-5 months waiting.

Regards

microlab