Why has the silicone become yellow?

This is directly related to the technology used in neutral cure silicones. All neutral cure silicones will yellow due to oxidation of one of the raw materials. 

The problem can be exacerbated if the silicone is in a dark closed room, away from daylight (UV). It can be reversed by exposing the silicone to daylight, but over time it will eventually yellow.

Removing and replacing the neutral cure silicone with another neutral cure silicone will not solve the problem.

The best alternative is to consider using an acetic cure silicone, which will not yellow. It's important to note though, an acetic cure product can affect substrates like natural stones and reactive metals. Consult the product's Technical Data Sheet for further information before using.