Environmental DNA Centrifugation: Pellet Pooling Peculiarities?

Greetings, everyone.

I'm currently optimising a protocol on eDNA extraction from freshwater samples for a species-specific assay. I want to test multiple workflows, including either filtration or centrifugation of water samples. (Both approaches have been previously shown to be reliable for the species of interest.) Here's the thing: for centrifugation, I plan to use at least 200 ml of water split into 50 ml falcon tubes. After centrifugation, the eDNA-containing pellets should be pooled into a single 1.5 ml microcentrifuge tube for DNA isolation. The thing is: how would you go about the pellet-pooling part? I've already tested it, and the best thing I've figured out is to carefully remove as much supernatant as possible and then gently aspirate the pellet into a large pipette tip. However, it feels somewhat unwieldy and I'm afraid this step may introduce unnecessary inconsistencies. If you have experience with this sort of pellet transfer and pooling, do you have any tips on how to get the best results possible?

(The already-published papers only mention that pellets were pooled, without additional specification. I plan to contact their authors to ask for details, but having some do's and don'ts from a larger number of people cannot hurt.)