I'd recommend keeping it in the same series and just labeling the episodes with a naming convention that shows where the arcs change. That way the subs you currently have can still receive notifications for each new update, instead from starting at square 1 again with a new series with no subs.
When I first started on Tapastic, I made the mistake of making each new issue release its own new Tapastic series. I don't recommend it. Readers were just confused why the series they where following didn't include the first issue and a lot didn't look to see on my profile the other Tapastic series I had at the time. It was a mess.
If it's within the same universe, using the same characters, with a story the current subs would appreciate, my advice is to keep it in the one series.