This article provides some clarifications on how merging of joints is handled.
On this page:
Joints merge only when moving or editing them. If you do not disturb the joints, they will not merge by themselves. The same is true if you import a model with duplicates – you can set the option to merge or not. Once the duplicates are in, they will not merge without some action.
If you disconnect joints, they keep the same merge number. You should then change one of them to prevent future accidental merges.