Usually, when working with CATIA and the PLM, the Bill Of Materials is updated automatically after each CATIA save via the PWB connector (e-BOM sync).
This is the case for all new CAD Documents created and modified in the PLM.

However, for the CAD structures coming from SmarTeam, the situation is slightly different.
Indeed, sometimes in SmarTeam, the BOM was manually managed or modified (Item manually added, quantity manually modified...) and to make sure that the migrated version of the BOM is retained in the PLM, no automatic update was triggered based on the CAD Structure. On the contrary, the BOM was rebuilt as it was in SmarTeam and it appears in the PLM as manually managed.
Also, since the CAD Documents coming from the SmarTeam have not been modified (saved) in the PLM during the migration process, the automatic BOM update has never been launched.

As a result, for the migrated CAD Structure, the BOM is set to manually managed. It means that for a given Part corresponding to a migrated CAD, all its dependencies (the BOM) are flagged with the attribute "Manually managed".
And then, even if a new version of this Part is created (manually, or because a CAD is versioned) the BOM will remain manually managed.

If you want to update your BOM, and to come back to an automatic update of the BOM after the CAD Document structure is saved in CATIA, here are the steps to follow:

1. Create a new version of the Part / CAD parent.
   Either manually create a new version of the parent Part from its profile card in the PLM, or create one indirectly from CATIA by creating a new version of the CAD Document. This will trigger a new version of the Part automatically (since the migrated Part versions are frozen).
    
2. From the new version of the Parent Part, edit the Profile Card and expand the relationship grid (at the bottom) and go to the BOM tab.
   There, remove all the ticks in the manually managed column.
   (Keep the ticks in the Pos & Qty Override columns if you want to retain this information from the Smt BOM)
    
3. Save the CATProduct from CATIA (or if already done, run the BOM Sync from the CAD Doc Profile Card).
    
4. Check the result.

And, if needed, refer to the previous version of the Part to see how was the BOM right after the Migration.
All dependencies in CATIA should be back in the BOM. If some are missing, there can be several reasons, such as:

    1. Some Parts might have been added manually in SmarTeam with no corresponding CAD Doc in the CAD Structure (e.g. glue): add them manually again in PLM (if relevant).
    2. Some components in CATIA are not Master, then their Part are not automatically added in the BOM: mark those as 'In-BOM' in CATIA and save the CATProduct again
    3. The BOM cannot be computed because your Assembly is not up-to-date (children with red dot) or the CATIA save window reports another error: check if your assembly is using only the current version of the dependencies.

See the FAQ below for more information on these BOM management processes. 
        
This process has to be done only once after the migration.
Once a Part's BOM has been re-computed once after migration using the PLM e-BOM sync, then each new CATIA Save will update the BOM.

More: BOM management in CATIA / PLM