exactly. I guess it was all happening in multiple "branches" - they used old stuff (pre-2000, including the Beavan album) and were re-mixing it, at the same time they were re-recording some parts, at the same time they were recording new stuff... I imagine that it all was happening in parallel and stuff was thrown in the mix all the time during the process.
that means two things - 1) it's simple to tell the (let's say) rough mix date - we usually have that one noted right on the CD. but it's almost impossible to tell when all the parts of the mix were actually recorded.
anyway. do we exactly know when Josh left and Brain joined?

Chinese Whispers say:
Last show of the [Primus] Australian leg was on 04/29/00. Brain would therefore audition for Guns in around May.

and news about Josh out of the band date to March.

that means one simple thing - the Rough Mixes #1-#4 are marked either from early 2000 or late 2000. they all are spread randomly around all 4 discs (we don't yet have the exact info from #2 but we can guess it's the same as the rest). at least the early 2000 stuff therefore can't have Brain on drums - as simple as that. we know that after Josh left, they auditioned some other drummers but didn't like any of them, so we can quite safely rule anyone else than Josh out - that means Josh is drumming on 100% of the early 2000 stuff (even though he was already out of the band).
we haven't heard the late 2000 stuff yet (still talking about the late 2000 MIXES! not recordings) - so there might be either Josh or Brain on drums. I'd say that it's Josh everywhere, but we still need to wait for the actual music, to hear if the late 2000 mixes sound the same as the early 2000 mixes and therefore it would be Josh everywhere.
the rest of the stuff is clearly either Brain (notes like New Brain Drums tell us that thing for sure), or it includes versions with both drummers to compare - and at that point we can know which of the drummers is there so we know roughly when the DRUM track was recorded. one could say that we would also be able to guess the recording times of the rest of the songs - but that might actually be not that easy. the rest of the songs might be recorded at any time by any lineup, and even if both songs will differ only in the drum track, we still won't be able to tell if the rest of songs was recorded in "Josh time" or later. the only way to tell would be only if the very same track would be included on the Rough Mix #1-4 discs.
huh. I think I overcomplicated it a bit, right?