Here is the way I do it on linux
1. Create a directory under my pictures directory with a name consisting of a
date in iso format and a brief description.
2. Copy the contents of the memory card to the new directory with the -a option
(archive preserves the file date).
3. Open digikam photo organ
Considering what rope-dancing is performed by SSD drive controller to
maintain homogeneous wear across disk space or what stunts happen on
modern COW filesystems with snap mechanisms etc. I don't see simple
fragmentation on exFAT as serious issue. Hovewer it could potentially
slow down the card