I have been able to resolve this issue:

1. Select enough amount of records into a new table

2. Truncate the original table as most of the records are redundant

3. Delete the original table completely

4. Change the new table back to the old name

The remaining question is:

As I do still need to replicate data from a linked server, I want to know what would be the best way to ONLY Select records from the linked server that are NOT in the existing table.

The table has a unique ID.