Initially Uru was built around the idea that all Ages are self-contained. In other words, a puzzle in an Age can NEVER interact with the puzzle from another Age (save for Journey clothes - these are your own, no matter which version of the Age you link to). But in Ahnonay's case, the game had to keep track of which sphere is currently active. Ahnonay's Cathedral uses this information to link you to the correct "sub-Age", and those sub Ages modify this property anytime you link back to the Cathedral.
There is another exception: Relto pages are also not self-contained! When you collect a Relto page, the game actually remotely accesses the game state of your Relto and enables the page. (This is very different from the mechanism used for Journey cloths.) DI has some hacks to make this seem to work; the Alcugs architecture makes this really hard to support properly. IIRC Ahnonay uses pretty much the same mechanism. (Under the hood, this is remote access to an age's SDL.)