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Sequence yellow exclamation mark, but nothing missing. A fix.
It’s been quite some time, but just ran into another occurrence of an archived Library brought back online, and seeing a yellow exclamation on a Project. I did find a missing plugin, replaced that, but still got exclamation. Close Library, restart X, yaddayadda, still have exclamation. Was in the process of making an empty project to paste current project into, and saw that the moment I hit Copy (everything in project was selected) the exclamation goes away. Had another project same library with the mark; selected all, copy – bingo – mark disappeared.
Guessing that it makes X go more “in depth” through it’s database in the process of copying & discovers “hey, it’s all here”.