the last time I customized I had to take my vendors down.
And there are some items you have to chop, like raised garden.
once you have those items chopped, you can costumize.
When you are done costumizing, there are certain items that will automatically go into the moving crate.
mine were usually goza mats, fireflies, virtue tapestries.
And usually whatever was on a tile that you changed.
They recently added a nice feature to containers... relocate container (on secure containers)
click that and target where you want to move it too
you will have to resecure it at the new location.
( I suggest if you are doing a big change to your design, move containers to the right side of your building.)
(then customize the left side. this way your contents don't get thrown in the moving crate.)
(or just customize one floor at a time, so all your contents aren't in the moving crate at once)