Steve,
The revised routes are almost all on chart 3462. This covers the entire San Juans and the southern Gulf Islands up to almost the northern tip of Salt Spring. This is a 1:80,000 chart that will serve for most purposes although you might want more detail for a few of the harbors. Unfortunately the Conover Cove area and the Telegraph Harbor area is just a bit too far north and are off the chart. You can add 3463, also a 1:80,000 and get this northern area.
For a more detailed view you could go to the 1:40,000 series. 3442 covers the northern gulf areas, 3441 covers the southern gulf area. You have to switch over to US charts to get the San Juans at the higher detail.
The trip through the middle of the San Juans is covered on 18434 and 18430. These are 1:25,000 charts.
I don't think you'll find you can buy single Canadian E-Charts in any format. I looked extensively last year and had to buy the entire region known as 'P1' from NDI.
C-Map sells this area as well in a couple different ways. If you already have the US San Juan Area which also includes the southern Gulfs, you can add the wide+ ($199) cartridge NA-C701 'Strait of Georgia'. This gives you the entire inside passage along Vancouver Island from midway up the Gulf Island north.
Another choice if you need the US as well is wide+ NA-C604 'Puget Sound to Vancouver'. This covers all of Puget sound from Olympia north including the San Juans and adds the Gulf Islands north to what looks to be about Nanaimo and across to Vancouver. It would cover the whole area on a single cartridge.
And a bigger choice would be superwide+ ($299) NA-C621 'Puget Sound to Cracroft Island'. This covers Puget Sound and the Canadian inside passage almost up to the northern tip of Vancouver Island. It doesn't go quite as far north as the C701.
Navionics Gold XL3 region 13 gives you all of the inside passage and puget sound for only $199 if your equipment supports these charts. It covers a larger area than C-Map C621 for less money. They are available on MMC or CF flash cards.
In the raster charts world region P1 will get you everything but the San Juan area is only at 1:80,000 detail. You can also get a S-57 for this area as well if you software supports these new vector charts. To get higher detail raster charts you can add what is known as region 15 in the US or go to one of the many sources that sell individual US e-charts such as
www.marineplanner.com. Unfortunately none of these sites sell individual Canadian e-charts.