Hi @ysh1962,
Comparing different projects that used different primers has been covered on this forum before, for example see this thread for various options discussed there.
In short, instead of trimming them you could use fragment-insertion tool which would allow to keep your reads as is. Or if you really do want to trim your V3-V4 down to just V4, you can use cutadapt to look for V4 primers in your V3-V4 set and trim it to there.
There’s another option of merging your separate reads after you assign them taxonomy then collapse them down to genus/speices. Personally I would rank these options fragment-insertion > trimming with cutadapt > merging at genus level.
Hope that helps!