How long would you say that it would take to get my Acolytes from Scintilla, in the Calixis Sector, to Juno, in the Askellon (SP?) sector ?

Take all available time intervals, sort them by narrative interestingness and filter the result by narrative convenience. Take the top result, which will be the most interesting, most convenient time interval. Go with that.

Alternatively take a time period that fits in your timetable, campaign or adventure. Travels through the warp can go faster or slower depending on it's "mood"

Depending on the ship (and other circumstances like the Navigator, the warp, the GM etc.) I would say somewhere in between a few months to a few years.

For fun, if your players are being sent somewhere to investigate a planet, have the warp spit them out earlier in time before the heresy has actually happened (don't let them know this right away) and see if you can have them inadvertently be the cause of the heresy that occurs.

Yeah, but then you get the ordo chronos involved, and that's a campaign in itself.

Yeah, but then you get the ordo chronos involved, and that's a campaign in itself.

Do they have a way of tracking when these things happen or do they just work by reports/deus ex machina?

We barely have a paragraph of information on them, so who knows. I'd suppose some of them have talents equivalent to the one you can get at the end of the Haarlock trilogy where you can notice time disturbances of the warp. They likely have psykers that can tell, maybe they work with eldar farseers?

Again too little info.

Yeah, but then you get the ordo chronos involved, and that's a campaign in itself.

The Ordo Chronos doesn't exist. That's what the man who called himself Doktor told me.

That man is a heretic and impostor.

Narratively, I'd say 1 week to leave Scintilla and reach a warp point in system (can't enter the warp close to planetary bodies), then roughly 4-8 weeks to reach the border of the calixus sector. Then another 8 weeks to travel through the scarus sector before reaching the Askellon sector and then a few weeks to reach the Juno system in the Askellon sector and again 1 week in system to reach the planet. All figures can be modified if the warp is especially active, leaving their ship either 'becalmed' or 'tossed about'.

More importantly is the fact that few navigators/ships still travel to doomed Askellon. Regular connections are unlikely to exist.

So it might make for a fun mini-adventure to actually find a navigator with charts to Juno. Maybe have the players hitch a ride to a space station/pirate haven whatnot in the calixus sector where they will then have to find a ship which can take them there. Or maybe they can find a friendly Rogue Trader with some berths to fill (unfilling those berths again might prove yet another adventure...).