I have been teaching myself rsync today...

[bodiebill]

Take care:

When using rsync

(1) all source files that have been updated will be copied over to the target (in an extremely efficient way where only changed parts of files are copied and if the file is exactly the same it is not copied over at all);

(2) all source files that have been deleted are deleted on the target.

Neither (1) nor (2) will be done when using --ignore-existing

Initial high disk activity could be the result of reading the source and target files.

Maybe you can monitor what is happening by adding --progress