The multiverse is a little confusing, so I’m going to try to boil this down as well as I can.
Generally, the “main” Batman books have only ever followed one version at a time, but it hasn’t always been the same version. The multiverse was created back in the '60s to explain why they’d introduced a new Flash and Green Lantern (Barry Allen and Hal Jordan, respectively). The then-current “main” world was Earth-One, and the original world from the '40s was Earth-Two (somewhat counterintuitive, but there you go).
It was decided that the heroes of Earth-Two had been aging in real time. The '70s and '80s saw a few books that took place on Earth-Two. All-Star Squadron was a period piece taking place in the '40s, while Infinity Inc. was a modern-day story focusing on that world’s second generation of heroes. Helena Wayne appeared there and in a few backup stories elsewhere, but to my knowledge never interacted with Earth-One’s heroes or had her own title.
In Crisis on Infinite Earths in 1985 and 1986, they merged all of the major worlds of the multiverse. There was now only one Batman, and he wasn’t old enough to have an adult child, so Helena Wayne was reimagined as the otherwise unrelated second Huntress, Helena Bertinelli.
The multiverse was recreated in Infinite Crisis (not the same event as Crisis on Infinite Earths, but sort of a sequel) in 2006 and its follow-up 52, but Helena Wayne didn’t come back at that time.
After the 2011 reboot, they initially got rid of Helena Bertinelli in favor of Helena Wayne, who’d traveled the main earth from her “native” universe. Later, they changed their minds and decided that Helena Bertinelli did still exist, and we haven’t seen much of Helena Wayne since then, but they’re both supposedly active at this point.