You could apply asking for discretion, see page 18 here for the requirement about absences in the last year of qualifying period for section 6(2) (if your wife wants to apply as spouse of a British national)
https://assets.publishing.service.gov.u ... retion.pdf
Absences in the final year
You normally only exercise discretion for excessive absences during the final year of
the qualifying period under section 6(1) if the future intentions requirement is met.
Where the applicant is applying under section 6(2) or has met the future intentions
requirement the following will apply. Total absences:
• of 100 days or less; exercise discretion
• between 100 and 180 days, where the residence requirement across the
qualifying period is met – discretion is only appropriate where the applicant
demonstrates strong links through the presence of family, employment and
their home in the UK
You would need to provide additional evidence of presence of family/employment etc in the UK or wait until her absences in the final 12 months before the application date are less than 100 days.
All advice comes from personal research and experience and should not be regarded as professional opinion.
