Steps to re-produce:
1. Make sure you have some branches in Subversion that are detected by Bamboo
2. Check that all of them are enabled
3. Make sure that the "Automatically manage branches" is checked with the default value of 30 days
4. Use a different path, other than default for the Branches Root URL (Ex. : https://seideh-xps13/svn/TestSVNRepo/trunk/branches).
5. Edit a branch repository URL to point to a sub-directory of [branch location]/[branch name] for example: https://seideh-xps13/svn/TestSVNRepo/trunk/branches/AnotherBranch2/SubSub
6. Notice that right after saving this change or on the next cycle of branch detection, the branch gets disabled.
Check the attached screenshot, both "AnotherBranch1" and "AnotherBranch2" got disabled after these changes.
- Changing the "Remove after" value to "0" days is the workaround to this problem at the moment.