OK - so f*k me
After reinstalling FlowerPot and OS4.1 - I tried again. Previously, I had unzipped the lha files for the updates directly on my Windows 10 machine, using 7-Zip. I had done it that way on my previous machine when I installed FlowerPot in 2020, also running Windows 10, without ANY issues. So I figured - this worked last time, should work again, right? Well, it did not.
This time, I decided to unzip the lha files on the AmigaOS using UnArc. Did it - and would you believe it, the update installed without any issue. Seems like the latest version of 7-zip is messing up (some) lha file. Or reinstalling OS4 did the trick. No idea.
Thanks for listening - this is (kind of) solved.