Sorry that I misjudged the stage of your project and I have been in your shoes and had to do exactly what you are having to do. Sorry for the challenges. Our products attempt to center on a continuity of service to the end user, so we populate the target with the bulk of the content prior to moving into the final stages of a migration which includes the switch over from the source to target. This permits a minimum downtime to the end users, resulting in a lower number of helpdesk calls and aggravation for you or anyone in your position.
We absolutely handle a number of shortcut situations including updating them to the new archive. Naturally, several situations are unique and if you or someone was considering us we would like to discuss the particulars of your situation to ensure we are a fit. It does not sound like you are desiring to do anything too far-fetched.
For FSA content, we have another migration utility centered on FSA called FSA Migrator. This is a lesser migrated content and the needs are specific, therefore we felt it best suited in its own product at this point in time. Information about this utility can be found here: http://evtools.net/fsa-migrator/
I know that shortcuts and FSA migrations are also something that common migration utilities are challenged with. I am really just an engineer so if you would like to discuss its specific use case for your needs and/or pricing I would have to get you in touch with someone else, but would be happy to do so.
Thanks for the interest and please let me know if you would like more info or anything else.
