I was wondering how to handle checkpoint numbers in a pipeline.

Assuming you have two separate SI projects you want to use in you pipeline.
Both shall be checkpointed before checking them out into different directories in the workspace. For better performance this is done in parallel.

How can I fetch the newly created checkpoint numbers?

The old plugin wrote the newly created checkpoint number into the "MKSSI_BUILD" environment variable.
Given the 2 parallel checkpoint processes this is very risky, as there is only one variable and 2 results. Which one will I get?