Depending on your version of Access you may find that Replication has been discontinued.
When I did this sort of thing, back in Access 97 & 2003, I added some special fields to all of my tables.
ID * - obviously the unique identifier of the record.
deleted - a Yes/No field to show whether a record had been marked as deleted. If you physically delete a record there is always a danger that it may reappear from an import at a later date.
dsChanged - a datestamp (Date/Time field) that is updated every time a record is changed.
When I imported data I would match the main data against the imported data by using the ID and update the records based on the newest datestamp.
* As far as the ID field was concerned I never relied on using an Autonumber because I wanted uniqueness across all of the copies of the database. Also Autonumber can be a bit of a bother when trying to add extra records from another source. I used to generate a range of Long Integers based on which building the database was in.
Given that the largest value that can be stored is 2,147,483,647 I figured I could have up to 213 separate databases each having numbers d,ddd,000,001 - d,ddd,999,999 where d,ddd represented the database instance. 426 if I used the negative numbers as well.
Building 1 would generate numbers 1,000,001 - 1,999,999
Building 39 would generate numbers 39,000,001 - 39,999,999
Building 67 would generate numbers 67,000,001 - 67,999,999
etc.
Of course how many records being produced a year would have an impact on this. If I had got close to running out of numbers I would have switched the database to use another range of numbers.