I think the best solution would be to warn when useless quantifiers are specified. (And, having formed this opinion, it is starting to sound familiar and I think I formed this same opinion the last time this came up.)

That is, /(?-i:hello)/i under -w should complain about something like "regex qualifier i applies to nothing and is ignored" (I hope someone can wordsmith that a bit) while /(?m-x:hi(?-m:lo))/x would complain twice. While /(?i:hi)/i would not complain.

Note that whether the ignoring of the flag has a practical impact is not important -- the warning is that conflicting flags caused flags to be ignored, not whether the flags had or would have had any effect on the regex parts they (would have) applied to.