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Can't compare databases anymore

I make a full backup (Via HeidiSQL) of a database on my database server (Linux MySQL)
On my development machine Win764 MySql I import this database under the same name. Database is running fine, all data present. Both databases are perfectly accessable by my applications and by standard MySql Tools.
Then I open Redgate MySql Compare (v.10.0.0.672 ) and fill in the source and target credentials. When I press 'Compare Now' the process stops on "Registering database one". When I switch the credentials it stops on "Registering database two". Both with the same error message: "Illegal mix of collations for operation UNION".
The database only contains tables, no views, queries, stored routines, triggers or whatsoever.
Why can't I compare these two identical databases anymore? It worked for years. (older or newest versions of MySql Compare don't make a difference)
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