If I re-create a database which was linked to a source control, it remains linked and showsconflicts
Please contact support@red-gate.com if you are still having this issue.
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This is currently expected behaviour, but we're still working on some of the conflict issues.
If you do not want your new db to be linked to the same source control as the originial one, then you should unlink it before deleting it or after it is re-created. You can unlink the db on the Setup tab once you have highlighted the db in the Object Explorer. (You can also choose unlink the db by right-clicking on the db in the Object Explorer and selecting Other SQL Source Control Tasks > Unlink db...
If you do want to keep the link to source control, but the re-created db is changed, then it will be better to unlink it and relink it so that it cleans up the underlying working folder. This may help resolve some of the conflicts you see.