Hello,

Unfortunately, there is no other way without a step of updating references in File B.

Just to let you know, updating reference models can be executed by using Command line also. Please read the astah* Reference Manual, 20.3. Total Merge Utility (P.316).
To open the manual, go to [Help] - [astah* Reference Manual] from Main menu of astah*.

- Note -
In the manual, it says "Please refer to total-merge-utilities.html for more detail in astah* Install folder." However we are afraid that the html file is not included in astah* professional 6.1 installer. The html file contains the same contents mentioned in the manual regarding the total merge utility.
If you have any questions regarding the total merge utility, please feel free to contact us.

The html file will be uploaded in the Bug report forum soon so you can download it.
We apologize for the inconvenience.

Sincerely,

Satomi