Tag's Lose Association from Linked Host

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We work on 360 primarily on MEP models, however, this problem I have is to do with the linked architecture model.
Our central model holds the MEP items, along with the linked architecture/structure etc. We use a builderswork tool that reads clash information (services going through walls) in the central model. We then apply the tool's findings to the architects model, where it physically cuts either rectangular or circular holes into the walls. When we 'reload' back in the central model, the holes appear and we can tag and dimension away. Job done.
The issue arises when the architects update their model. As soon as we receive it, we reapply the holes to the model, then link it back in way of 'reload from'. As soon as this command has completed, all tags lose association to the holes and end up looking like a question mark. All dimensions are also deleted.
I wouldn't mind if there were only a handful of holes, but it's a different story when you have nigh on 500 and every single one needs another dimension adding in and the tag re-associating.
Anyone had anything similar or know of a fix?