The problem is that when exporting a job, all the prior “dependencies” in the workflow are exported too.
The solution is to first get rid of these by inputting your extract micrographs job (for example) into a particle sets job (setting the batchsize to an arbitrarily large value), and removing the location slot from the expanded inputs (which will remove the micrographs from the outputs).
Now when you import the job using your first described method, it should just copy across the particle stacks, not the mics.
Hope that helps!
Cheers
Oli