Considering the radically different animation styles between MODOK and Hit-Monkey sure how that would've worked (maybe that's why it was dropped?).
Generally when there's a crossover between two different animated series with different design styles, the guest characters are redesigned to fit the style of the "host" show, like when
The Critic's Jay Sherman appeared on
The Simpsons, or when the characters from
The Zeta Project appeared on
Batman Beyond. I recently binge-watched
Marvel's Spider-Man on Disney+, including his guest appearance in a 2-parter on the animated
Guardians of the Galaxy, and in the latter show, they drew him with a slightly less cartoony and considerably more muscular appearance, as well as rendering one of MSM's primary locations (Horizon High) in GotG's more realistic (and surprisingly beautiful) background-art style.
Although I've seen the occasional instance where the characters kept their own designs. There was one case -- I think it was a crossover between
Kim Possible and
Lilo & Stitch: The Series -- where the characters all kept their original designs, and the contrast in art styles, line thicknesses, etc. was jarring. And then there are some productions that embrace the difference in design styles and use it in the stories, like in Nickelodeon's crossovers between the 2D
Fairly Oddparents and the 3D
Jimmy Neutron, where the characters took on each other's animation style when they entered each other's universes and remarked on the change.
So if we're talking about a separate miniseries teaming up characters from multiple different shows, it's hard to guess what they might have done.