The meaning doesn't really change, but the stress on "was" becomes a bit unnatural, like "They don't like you, they like them". We do accept that option, but the basic one is definitely better.
With these personal pronouns, there is no change to the genitive case when using negations?
There is, but the genitive is nearly always the same as accusative. Compare https://pl.wiktionary.org/wiki/Aneks:Język_polski_-_zaimki#Zaimki_rzeczowne
The change is only observable in 3 person singular feminine, neuter and 3rd person plural non-masculine-personal.
Why is it that "They don't like you all" isn't accepted? Since 'was' is the declination of 'wy'
Well... that's rather surprising, "you" is absolutely needed here and if it really wasn't here, it would be a huge bug. If you see it again, can you take a screenshot, upload it on any hosting website and post the link in the comment?
Yes, it is, unfortunately I didn't think of it at the time and I use the duolingo app on my phone not on my computer. Also, I've moved past that particular question and that lesson.