Mixing Sample Rates in Traktor S4 & Vinyl transfer Advice

I am currently digitising my vinyl and loved the 24bit/96khz but at around 125mb for flac per track it's not a great option.

I would like to put them to 48khz/16bit because they do sound better than 44.1khz, but will this adversely effect Traktor using traditional 44.1khz mixed with 48khz?

Additionally would Traktor be happier with wav over flac? The wav's I've bought and downloaded from Trackitdown have behaved perfectly but some of the vinyl transfers have been temperamental with tracks jumping (I think that was down to having beatsync enabled and the beat markers drifting due to the inaccuracy of vinyl)

Any advice from seasoned users is appreciated :)