Bamboo should finish "Force Clean Build" operation before it starts doing the checkouts.

Consider the following Source Repository Checkout task:

Repo 1: GitHub
Folder: Parent

Repo 2: SVN
Folder: Parent/Child1

Repo 3: GitHub
Folder: Parent/Child2

The task will checkout the repos in the following order:

Repo 3
Repo 1
Repo 2

This results in the checkout of Repo 3 being deleted and the subsequent tasks that work on it failing.