Repairing Invalid Configuration
Git keeps the configuration values for a Submodule in various places (e.g. in .gitmodules, the local .git/config, the Submodule's own .git repository folder...).
When not using Tower for adding and managing Submodules, it can easily happen that these configurations get out of sync - and become invalid. Tower highlights this status in the sidebar and when selecting such a Submodule:

In such a case, you have two alternative options:
- Completely and cleanly the Submodule
- Use Tower's functionality to try fixing the invalid configuration