I typically butt stitch the ends of the halyard and messenger lines together and then put masking tape over the joint to smooth it. When I was working as rigger and over the years, I replaced a lot of halyards and it was amazing what could and does go wrong. I would advise against Mr. Christian''s (and I am not picking on Mr. Christian per se) suggestion doing a tuck through the line and tieing the messenger line without taping over the loop and knot. That was a very traditional way to re-run a halyard and that is the technique that we used to when I first landed the job as a rigger BUT we had a loop of line catch on what we speculated was the end of a bolt or screw and we were not able to free it for days. When we did free the halyard the halard went one way and the messenger line went the other so we were forced to fish the halyard down the mast.
The second point is about tieing vs splicing. While a splice are nice, it really is not necessary and may not be the best idea for distance crruising. Most halyards are sized for minimal stretch, adequate life after chafe, and for comfort in gripping rather than working load capacity which means that they have many times (typically 3 to 4 times) the load capacity required to break the line as compared to the actual loads that they expeience.
Knots typically reduce the strength of the connection by 20% to 50% depending on the type of line and type of knot, so the lost strength at the knot is negligable. What is nice about using a knot vs a splice is that you can easily relocate the halyard attachment point at sea as the biggest source of chafe is in the first couple feet of the halyard where it passes through the masthead sheave. If you do tie on the halyard shackle, it and you are using a double braided line, it is important to stitch on a whipping, rather than simply burn the ends of the line so that the core can''t retract into the shell. With double braid I typically add a sacrifical cover at high chafe areas and at the halyard locks of cleats. To do this I buy some line (any cheap double braid will do) in the next larger size, strip the core and slide lengths of the cover over the line until they are centered on the high chafe area. I then split the ends of the sacrificial cover and tuck the ends of the sacrificial cover into the cover of the halyard and stitch it in place. I then pull both the halyard and the sacrificial cover tight and do the same at the other end. This greatly adds to the life span of the cover and reduces slipping (experially with smaller diameter high tech line)at the stoppers and winches.