Did you replant them one by one? They can’t be put in storage so did you replant them somewhere temporarily first and then replant them again? Or did you chop off all trees and sold all flowers then just planted from seeds and saplings?
i chopped a lot of them down actually bc i figured i could just replant them whenever! it makes it a lot less overwhelming. otherwise, for those i didn't cut down, i built around those trees first and then if i wanted to move them, then i kept a good amount of them in my inventory so that i could slowly replant them someplace else! a lot of running around but you feel super proud after you've done it all. i have plenty of coconut trees so if i had to move them then i'd just eat fruit. when i moved trees to make an orchard, i just kept as many trees as i could in my inventory and slowly moved them to the place i wanted them to go.
i always eat fruit, scoop everything up and sell it if its easily replaceable, everything else goes on the beach or out of the current way. i do like building around trees sometimes though, it does encourage you to think out of the box and helps give your island a more natural, organic feel, i think!
I replanted them somewhere else since it's easier to buy fruits and plant them at the intended places again rather than buying trees/sapling and waiting 3 days for them to grow.
For flowers I would trash them unless they're hybrids or those that I can't obtain on my island without waiting for Leif.
I chopped all but my fruit trees, I placed them all in a little orchard, then changed them to the real orchard when the space was ready. My flowers were a mess, I put them all in a big field until I decided to sell most of it.
I relocated some of my trees and flowers, but I just trashed a lot of them. I placed a trash can near one of my villagers houses. Sometimes I run over to his yard so I can trash a bunch of trees and flowers!
moved my native cherry trees down by the beach [they were going to encircle my house].
shook all the non-native trees down and chopped them up and planted new ones in their respective areas [a mixed apple orchard and orange grove, and some peaches and pears by a little pond].
There are 4 possibilities for me: 1. Move them to the place where i don't terraform
2. Cut them down
3. Put them in my pocket space and keep them until i know the place to replant them
4. Sell them