For https://docs.moodle.org/en/Course_backup and https://docs.moodle.org/en/Course_restore the platform doesn't matter. Of course the Moodle versions should not be far apart, specially not backward. If you really mean course data, not taking users and their work across the platforms, there shouldn't be problems.
Or, did you mean a https://docs.moodle.org/en/Moodle_migration ?
As a by-product, going from Windows server to Linux, you'll be a happier person!
Backup and restore
Backup @WIN and restore @LINUX 2.6
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