Are you using views placed from an AC project? As opposed to placed PMKs or something.
If so, 'Read All From' is your enemy. To link to project views, the button has to say, 'Link To'. 'Read All From' wants a folder containing drawing files, not a PLN, as you have seen.
Ideally, you should be able to select all the views in drawing usage, click 'Link To', and choose the PLN. I don't understand the particulars, but some conditions (deleted drawings? views from different projects?) cause the button to switch to R.A.F. instead, which is
useless
for view linking.
When you hit this snag, try selecting small groups of list items, while watching the 'Link To' button, to isolate the bad actors. Then link them separately. Note: you'll get 'Link To' for them by themselves. I don't get it.
OK, setting up templates. Make view sets in AC. Save the project as a Project Template (.tpl). Make the layouts and subsets in the layout book, and import the views from the template project into their proper layouts. This becomes the 'book template, though there's no special file of that type.
Start a new project with the template, and a new layout book from the 'book template. Select all the views in drawing usage, and Link To the new project.
It should work. If there are bad links in the templates, isolate and fix them before releasing the templates to the wild.
HTH,