Hi Adam,
I can certainly sympathize with the segment management issue you are running into in re-adjusting the 'base' report suite. For your specific use case the steps can at times be confusing and lead to unintended segment logic saves. I would chalk the issue up to the major UI transition that occurred when segments moved from being only ever tied to the report suite they were created in originally, to the new paradigm where segments have a 'base' underlying report suite, but can be applied across any report suite.
My sense around the product intent around Segment Manager is that it allows for group management of segments for only a strict set of actions: descriptive tags, share, deletion, approval, and copy. There is also the option to rename if only a single segment is selected in segment manager. As such the function of segment manager does not allow for the editing of the actual query logic within multiple segments because then there would be potential conflicts when certain segments had different 'base' report suite setting definitions and the segment manager operates in a environment where no one report suite is active. That I believe is the reason why segments need to be anchored and altered from a specific user designated report suite environment in the UI via segment builder.
I do agree that it would help if there was better 'base' report suite indication within segment builder/segment manager which could aid in identification and altering of segments (there is the initial RSID filter selection by default tied to whatever report suite the user is in). I do see however the counterpoint since segments are universal and apply across report suites recognize that there are also potential downsides if the segment always switched back to the base report suite every time it was selected to be edited in segment manager and sent back to segment builder. It would take away from the utilization of segments as universally applicable in some work views and potentially add confusion. In general RSID selection is always at the discretion of the user in terms of their explicit selection and to my knowledge there are no RSID selection 'overrides' via UI actions. The decision around segment and RSID pairing handling was one of the most difficult by product in my view, but had to be done because the workflow good outweighed the conflicts and incorrect logic cases across incompatible report suites.
I think the best option right now is to follow the Customer Care suggestion to do all your segment alterations from the desired 'base' report suite. This does require you to go through each report suite environment one by one and does not allow for any quick group management via Segment builder selection. I would add that adding tags which label the 'base' report suite might be a way to help organize and record your progress across report suites. Hopefully in the future since all new segments will be created in the desired report suite, you won't run into this issue again since they will be universal from the get go and not require any back 'base' report suite resetting. Therefore your current work where you are running into these RSID resetting issues would be a one-time exercise to transition all your segments to the new method of handling and management.
Best,
Brian
