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This seems to be related to issues relating to menu/features
See #860974: Menu Links will not import/revert where @Grayside suggests:
menu_links being a poorly implemented system, you might need to manage them via update hooks and leave them out of your Feature export
However there's also a feature request for #968826: Export Menu links with UUID
Comments
Comment #1
lightsurge CreditAttribution: lightsurge commentedPatch here requiring uuid module
#1283742: UUIDs for Menu Links
Comment #2
lightsurge CreditAttribution: lightsurge commentedSimilarly this breaks the contexts which rely on these menu items.
Comment #3
jgraham CreditAttribution: jgraham commentedComment #4
jgraham CreditAttribution: jgraham commentedComment #5
jgraham CreditAttribution: jgraham commentedUUID menu links was removed from the latest uuid. This is moving towards uuid_path and possibly the deploy module, but nothing is quite stable yet.
I think I have resolved the issues regarding these cases, if that's not the case please re-open with details on how to reproduce.