Yes. I lost half of my hybrids from TTing back and forth (day-by-day, mind you). :/ I didn't have the beautiful town ordinance on though; if you have that town ordinance on, they won't die (I haven't tried TTing over more than 2 days at a time though).
Any amount of time that you go BACKWARDS will always count as one day in the game. So even if you go back 3 months, the game treats it as if it was only one day. Forwards is different. So if you go forward 3 months, it counts as if 3 months have passed. This is a weird concept to explain, and IDK if I did it well.
But the point is that as long as you go backwards in one leap, then log in and water your flowers, talk to villagers etc...it should be fine. Don't go backwards one day at a time, unless you're going to stop each day and do all that too...like you would if you were playing normally without time travel at all.
Also, if you can just put the beautiful town ordinance on, then you don't have to worry about flowers dying at all.
- - - Post Merge - - -
Oh also, you can put the flowers in your locker or inside your house if there's any you're EXTRA protective of. But really backwards TT-ing one time shouldn't hurt anything, since it's only 1 day to the game.