Frame-by-Frame Lip Sync + Interlacing = ?

[AngelOfTheDark]

So, my predicament is, no matter how much I play around with filters, changing variables, filters, etc, I don't like the deinterlaced footage of FLCL. In fact, the only footage I like is the .vob files ripped straight from the DVD. I have also found that I am among the lucky few who are able to edit directly with the .vob files without anything really going wrong (it usually doesn't even slow down my computer all that much). I've already made several nice-looking videos this way with interlaced footage, including one using FLCL. But this time I'm doing frame-by-frame lip sync (where you take one frame of the closed mouth, repeat it as necessary, then one frame of the open mouth, repeat as necessary, etc.) Before I start to get into this really really long and complicated project (complicated because there are some parts where I want to use my overlay tracks to lip sync more than one character at a time), I was wondering: will mixing the strings of single frames without interlacing with a few strings of interlaced footage (for the parts that aren't lip-synced) mess up the final project? Particularly if I play with the quality after editing? I mean, I know I have to be careful about resizing and certain effects, but other than that. This probably is a strange (or perhaps stupid) question, but I'm still trying to teach myself all this technical stuff.

Oh, and I don't know if this is relevant or not, but if it turns out well, I intend to enter it into a convention contest.