When working with linked/cross-referenced parts, there is one additional step you must perform (after editing and/or saving the assembly) to ensure your edits are stored in the linked part file: you must push your edits to that part. The "Push edits to linked components..." is the Bommer command that actually modifies the linked part, creating a new version of that document and updating the reference within the currently opened assembly. This step finalizes the editing process for linked components.
The "Push edits to linked components..." command
The "Push edits to linked components..." command appears in the Bommer dropdown menu when there are edits to be pushed to linked components (when there are edits that need to be pushed, the "Edit bill of materials..." command icon will also change to ). Click on the command in the menu to open the command dialog.
On this screen, you can control which linked design you want to push to (or click the top checkbox to select all of them). You can also control whether or not Bommer should save the documents after editing them (vs. leaving them open), or if the push operation should open documents silently. Note that unchecking "Commit all changes?" but leaving "Run in background?" checked may lead to strange/undesired behavior; generally, you either want to run in the background and commit all changes, or make sure Bommer opens the documents to be visible in Fusion so you can inspect the changes before they are saved. Once you press OK, Bommer will open, edit, and save each document that is checked, and then update the references in the open assembly. You can then save the open assembly to save those reference updates.
Automatic edits when opening a document
Alternatively, if you open a linked document that has edits that have not been pushed, Bommer will automatically update the bill of materials data for that document; then, when you save the document, those changes will be saved as well. This is as functionally "as good" as pushing edits from the assembly, in a different workflow. In either case, if you cancel the operation (by either canceling the push edits command, or closing an automatically edited document without saving, the edits will not be lost; you can re-open the push edits command or the document(s) when you are ready to push those edits to the linked component(s).
Fusion 360 must be online to push edits
Due to a bug within Fusion 360, we cannot open documents to be saved from Bommer when Fusion 360 is in offline mode, and so we cannot push changes in this mode. You can still open the document, let Bommer apply the edits, and save the file yourself; or you can switch to online mode and use the Bommer push command.