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External System Integration by SfID with Merges

Does anyone have recommendations on how to connect data between salesforce.com and an external system by salesforce ID and account for record merges?
For example, the amount of space provided for attachments by salesforce.com is not sufficient for our needs especially since there is no option to set a user/profile/role quota.  As a result we're starting to develop a salesforce.com driven external document store (via an ASP.NET application run though an inline scontrol) based on the salesforce record id. 
Since the salesforce.com record id would be the primary key in the database - when our automated de-duplication process are run the "losing" or deleted record from the merge would also lose (technically orphan) all of it's associated documents since the history of this id is not recorded in the new record.
15 vs. 18 character ID limiations aside this integration is very easy to do withour worrying about merges but once merges factored in I'm stumped on how to move forward.
You can use the masterRecordId field and the QueryAll call to find out which record the mergee was merged into.