Moving Data Between Databases

I have a web app that has been regulated to a disconnected PC. It's runing IIS and 2.0 with sql server express, but no connectivity. I have changes that are made to some of the data in the db (data, bot schema). There is one particular table that I cannot overwrite, and must extract the data.

What methods are available to do this swap of data between databases? I was thinking of doing something like this:

Track last date that remote db was updated. Upload updated database into data directory, loop through records for all affected tables, any date that was past logged date then update the record if it exists or insert new record, and then loop through the remote db and delete this records that dont exist in the updated db.

This seems intensive and slow - especially as the tables get bigger but I can't think of another solution that can be done by a user using sometime of web interface.