I suspect that you've been running uncoupled, and didn't remember to re-couple before finally saving the project.
DG
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You haven't always worked like this. You already said that you switched projects. You don't usually do that, so this is what has changed. So what we need to know is how you switched projects in the first place, whether or not you run uncoupled, whether or not you load metaframes before you start Logic.
DG
Yeah they would do, I suppose. My view is that if VE Pro is a supported host it is the plugin developer's responsibility to make sure it works with that host. Anyway, that doesn't' help you.
Unfortunately I can't replicate your set-up, so I don't quite know where it has all gone wrong. My workflow is (always running coupled, and all instances saved and Preserved):
Never had a problem. I don't know whether or not that helps you at all.
DG