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I am using ODBC driver to connect SQLite to Power BI (or excel). The issue is Int64 value is truncated to 32 bits. F.x.:
6269010728497363496 = 0x5700000AFD32BA28
-8358680861215162072 = 0x8C00000AFC6A0128

are presented as
-47007192 = 0xFFFFFFFFFD32BA28
-60161752 = 0xFFFFFFFFFC6A0128

The data type set to whole number in P BI that is Int64

How to fix the problem?

What exact version of the driver do you have? Please send the DDL script that creates a table where the Int64 values are stored.