It's for a simple shot where I have duplicated somebody and cropped half the screen to make it appear as if the subject is jogging next to her twin.

I've tried the keyboard shortcut (Command L) the drop down menu, a new sequence and even creating the shot in a new project but I can't, and have never been able to link layers. The option is not even highlighted in black on the drop down menu.

This means that the only way I can flatten these layers into one so I can perform a motion glide/zoom is to redo it in a separate project, compress it to QT 1080-720 to achieve maximum quality and put it in the bin as another clip.

I don't mind doing this and little quality will be lost but I can't help wonder in what situation I would be allowed to Link Layers.

Maybe I'm not following what you want to do, but wouldn't you just create a new sequence that is just your layered effect, then embed that sequence in the primary sequence timeline? That way if you want to tweak your layers, you do it in the layer sequence ..?

Cheers,
GB

Do you mean nest the three layers in a new sequence?

I did try nesting, but I need the layers flattened into one as can be done in Photoshop.

It's not a big deal this one, as I ended up compressing the multi layer sequence in Quicktime and using the compressed file. It's still a mystery as to why the link layer option appeares to be there in the first place if it's not allowed.

What you're trying to do can be done by nesting in FCP, precomposing in AE or nesting layers in Motion. But it sounds like you want it to work like it would in a nodal compositor. So maybe you should be doing this with Nuke?