For what it's worth, some bunnies naturally drink a lot more than others - when my girls were young and I still used a water bottle instead of bowls, I could tell from the next room which bunny was drinking because Nala would get aggressive with the bottle and chomp on it. Overall, Gaz seemed to drink 3-4 times as much water as Nala (Gaz also ate a lot more leafy greens; picky little Nala didn't eat much veggies at all) even though their weights were very similar - the difference seemed so significant that I got paranoid enough to take them both to the vet for urinalyses. $70 or so later, I found out that both girls were perfectly healthy. A healthy rabbit will drink however much water they feel they need to, and that amount can differ significantly from rabbit to rabbit even when they're similar sizes and have similar veggie intakes.
Imo, separating them to monitor water consumption is pointless since comparing one rabbit's water intake to another rabbit's will NOT tell you if one of them is drinking an excessive amount or isn't drinking enough. The only way to determine if their water intake is a sign of a health problem is to compare a bunny's current intake to their past/previous intake (in other words, a sudden increase or decrease in water consumption relative to that particular bunny's "normal" amount would indicate that something might be wrong); even then, you have to take into account the water they get through leafy green veggies (especially if they're fed to the bunny while still damp from being washed). If you don't know how much she typically drinks when healthy, then you don't have a "control" to compare her current intake to and the data (about water intake) obtained by separating and monitoring is meaningless.
Oh, and if you do a "tent test" to check for dehydration (pull up the skin between her shoulder blades to see if it goes back into place pretty quickly), that could confirm that there's an issue but can't confirm the absence of any issues.
As for the half-sized poops... they're not necessarily indicative of an issue, but they could be. Some of it depends on the quantity/frequency of odd poops and whether the bunny's poop goes back to normal pretty quickly. While it may not end up mattering, it certainly can't hurt to determine which bunny the abnormal poops are coming from so that if you continue to see them, you know which bunny is having issues.
In other words, while I think it's pointless to separate them to monitor water intake, I actually think it would be a very good idea to separate them for poop-monitoring purposes. I recommend using Tauntz' suggestions about how to separate them
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Guide to bunny poops
[Btw, you always want to take both bunns to the vet together if they're bonded even if the second bunny doesn't "need" to go - if one comes home to the other smelling like "weird vet's office" it can definitely upset their bond... perhaps Rosie knew that when she coerced you into bringing Jim along
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Edit: by the way, have you had the bald patches checked out by your vet to rule out mites as a possible cause? (I don't remember off-hand if you've got a separate thread somewhere about the bald spots.)