What does it mean when your epoxy hardener comes out coloured? Will it put your project in jeopardy?

Nope. It turns out that this is not really a problem for strength or curing characteristics, only for appearance.

The makers of West System epoxy say that a colour change in the hardener, commonly to red (for 206 Slow) or orange (for 205 Fast) is a normal reaction to extended exposure to air and moisture. Their tests have found no appreciable reduction in strength when using coloured hardener.

It does, however, look a bit ugly, so for cosmetic surfaces I'd continue to recommend using a fresh batch of clear hardener (type 209, if you're using West System).

One of the joints shown below is with old West 206, the other with old West 205. Both hardened up just fine and I'm not worried about the strength of either joint. They are, however, far from being show-worthy; it's a good thing they'll end up inside a sealed crossbeam structure.