Absolutely take the kids on the day trip to see their aunt. I'd be more concerned I'd run out of gas before a couple of 6 year olds! Catch a really early train (they can sleep a little more on the way to Paris if they need it, but most kids love riding trains) and take a late train heading back.
As long as you (and your sister) don't have some crazy minute by minute packed schedule lined up of "must sees", you can manage your day however you want. Walk around a few different neighborhoods, visit Luxembourg Gardens or Promenade Plantee, check out one of the outdoor markets, stop for a long lunch. Get a view of Paris from the top of something (doesn't have to be the Eiffel Tower with its timed tickets and entrance fees - take them on the funicular up to Sacre Couer and look at Paris from that vantage point). See part of a less famous (hence less crowded) museum that might be interesting for the kids - like the Gallery of Evolution or Virtual Reality room in the Natural History Museum. Stop somewhere for a hot chocolate. Hit up a shop that sells many flavors of macarons or pick out some other pastries to go and then take a boat ride down the Seine. Have an ice cream at Berthillon.
They won't remember everything, but it's kind of surprising how some little details of a single day can stick in kids minds forever. One of my friends has 2 girls who are now older teenagers, but when they were 7 and 5 years old I took them around Boston. They still talk about how we all sat sketching with colored pencils at the Museum of Fine Arts (the older one said that 1 visit really got her interested in art, and now she's been accepted at RISD). The younger one talks about how she remembers us ice skating at Frog Pond after the museum and that we ate both a cheese fondue and a chocolate fondue in a single meal. You've got a nice opportunity for your kids to have a great memory about spending time with you and your sister. That's worth the cost, the time invested and the sore feet and long nap you might have the next day.
