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With the 5.0, I got these warnings:

warning 6035: The relationship 'VCL.R_313' has columns that are not part of the key of the table on the primary side of the relationship which is not supported, the relationship was excluded.

This was not a problem in 4.75.43.

I also noticed that this occurs when the foreign key was nullable.

This warning is arised when the EDM is generated. This is a limitation of Entity Framework.
Probably, some changes were made in mapped database objects, because this message has to be shown in 4.75.43 too.

I actually generated Edmx from both 5.0 and 4.75.43 from the same database and compare the results. 5.0 has these warnings and 4.x does not.

I have two machines, one with 5.0 and one with 4.x just to compare the results.

Please provide us the script of foreign key that causes the error, and the script of the tables taking part in this FK.