So I have some footage shot on mini dv tapes and digibeta tapes as well.  My boss insists that everything be digitized at dv50, but our mini dv decks can only digitize at dv25.  And on top of that, we export these as dv files, which I believe can only export at dv25;   

Does it make sense to have some footage at dv50 and other footage at dv25...mxing resolutions? Or should I just keep everything at dv25? 

You should actually NOT capture it as DV50. Taking it in via firewire natively means a bit for bit copy of the data. This is as good as you can get. Capturing via SDI or component (cause you cant do a DV25 to DV50 via firewire) and using DV50 compression increases compression damage. It is DV25 or uncompressed is your only option here.

You could capture the Dig Betas at DV50 to preserve some quality.

I'd love to know if you can get it to work! I couldn't...

JC