Does cloning a hard drive mess up programs?

I have a SSD with windows on it, and a HDD with all the data and programs. I want to get a bigger hard drive. So i want to clone my hdd to a new one.

I want to use Western digital acronis, but i have a bad feeling that some files on my sdd will be confused because all the program files on the hdd will have a new location.

Does that make sense?
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More about cloning hard drive mess programs
  1. i have no idea why i put this in motherboards
  2. Best answer
    as long as the new clone drive have the same drive letter. It should works fine.
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