Validate data between two large tables
Transactional Replication.
As one idea, this sounds like a reasonable candidate for transactional replication. Checksums, cyclical redundancy checks (CRC), and row counts are used to validate source data with the destination data.
From Validate Replicated Data, Books Online:

How Data Validation Works
SQL Server validates data by calculating a row count or a checksum at the Publisher and then comparing those values to the row count or checksum calculated at the Subscriber. One value is calculated for the entire publication table and one value is calculated for the entire subscription table, but data in text, ntext, or image columns is not included in the calculations.
While the calculations are performed, shared locks are placed temporarily on tables for which row counts or checksums are being run, but the calculations are completed quickly and the shared locks removed, usually in a matter of seconds.
When binary checksums are used, 32-bit redundancy check (CRC) occurs on a column-by-column basis rather than a CRC on the physical row on the data page. This allows the columns with the table to be in any order physically on the data page, but still compute to the same CRC for the row. Binary checksum validation can be used when there are row or column filters on the publication.