When a magician creates an astral form like a sustained spell or a ward, there exists a link between the creator and the form that can be traced. And the nature of the form is related to the aura of the creator. But what happens when the creator of the astral form has the power to Mask her aura, either through the Masking/Extended Masking metamagics or through the Aura Masking spirit power?

When the link is through a sustained spell, it seems to me that the link must remain, and therefore must somehow reflect the change. How about when the astral form sustains itself, though? For example, a ward or a Quickened spell. Once they are up, the creator of the astral form can Mask his aura to look like something else. Do the self-sustaining astral forms also change, or remain as they were when they were first created? And if the latter, are they no longer usable to seek out the creator?

Neither Masking nor Flexible Signature have an effect on tracking somebody through an astral link (see the see the table of Astral Tracking modifiers), so I'd say no

The first item in the Astral Tracking Table is the pertinent point: "Each hour passed since astral link was active". How does the change from an aura 'oranges' to an aura 'apples' affect that active link, when the original astral form is still 'oranges', but the creator is now 'apples'?

I just bury the links in the Astral Plane. Any Trackers have to make an Astral Quest at that point to figure the link out.
Assuming that the Magician has Initiated at least once, of course.

The creator always feels if a ward is attacked or a quickened spell is dispelled, therefore the astral link obviously remains active as long as the ward/spell exists.

Yeah, I can see a number of ways things have to stay connected.

One problem that just dawns on me is that, if the links stay active, you can have an aura of 'oranges' but a link leading away from you with a taste of 'apples'. So much for Masking your true aura if you have any astral form up and running that was created before you covered your aura.