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SQLite diff tool doesn't work with CRLF new line characters
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(Edited to reflect new sqldiff behavior no longer optional.)

The sqldiff utility, in its latest form (on the trunk branch as of https://sqlite.org/src/info/ff74c0cc4cefa527 ), has a new behavior for its normal output (which is SQL to bring named DB's to sameness.) It renders text field values that are to be updated or inserted in a form that should not suffer the ambiguity of non-graphical characters being treated in special ways that has (probably) led to or contributed to the OP's problem.

Now, these sqldiff invocations will show differing line-endings or other less visible control characters that make putatively identical databases not quite identical. For example, where line-endings are CRLF in one and LF in another, running<code>
   sqldiff test-copy.db test.db
and
   sqldiff test.db test-copy.db
</code>will visibly show the difference in those control character sequences.

BTW, I still recommend newline normalization for the OP's situation. The sqldiff change makes problems such as his easier to see and remedy, but newline normalization would side-step them altogether.