Right now Azure Data Sync is applying changes to tables in alphabetical order, which is also the same order we added the tables to the schema. This is causing issues because a child table is loaded before the parent and it hits the 1000 error limit. We work around this by manually syncing the parent. If we put the tables into the schema in the order we would like it to apply will that fix our issue?
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One scenario that could cause this error is that the foreign key constraints are defined in the destination database, but not in the source database.
First step is to check that the referenial integrity is defined indentically on both databases.

Shiraz Bhaiji
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This is correct. Our source DB has very few FK defined so we can replicate the data back – Scott Thompson Feb 11 '20 at 17:19