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I successfully followed user613363's recipe to this question to set up a dual-boot system with Windows 10 and Ubuntu 18.04. Now, I need to move my Windows 10 installation to an SSD (replacing the current disk) by cloning.

What steps will be necessary afterwards? Do I have to update the boot loader? If so, how? Are there any obvious pitfalls that I should avoid?

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After successfully moving Windows 10 to a new SSD while preserving the dual-boot setup using the hints given in the comments, let me post a summary as an answer.

Starting point:

  • Ubuntu on HD1
  • Windows 10 on HD2 (500 GB)
  • Empty HD3 (500 GB)
  • Ubuntu on flash drive

Steps:

  1. Disconnect HD1 to avoid any accidents
  2. Install HD3
  3. Boot into Ubuntu Live and use GParted and dd as discussed here to clone HD2 to HD3.
  4. Once dd has completed, shut down and remove Ubuntu flash drive
  5. Disconnect HD1, reconnect HD2

At the end, both installations (Ubuntu on HD1, Windows 10 on new HD3) can be booted from GRUB as before.