Hi, @johtso and @dpcY. We do explain a workaround for this in the support guide below:
Quoting:
4. You can use this workflow with multiple private submodules attached to the same repository, but that does take some extra work since GitHub does not allow Deploy Keys to be used in multiple places. You’ll have to instead add them to a user (perhaps you? or maybe a robot-account that you create on GitHub) that has access to all repos.
Will that solution work for you? If there are other questions, please let us know.