@Pachanga
Once you have have S-Off then you should be fine. As it's still in beta, AlphaRev are still tweaking things (especially Windows), but as you've got through the actual process, it's unlikely you'll get any problems because of it. So, once it's successfully finished, you're safe. The problems you will now have (if you want them!) is regarding which ROMs to flash and if you need to return your phone under warranty.
There is a proviso to this. Currently, AlphaRev only works with one version of HBoot. AlphaRev claim to have protected users from overwriting HBoot so that it's not possible to flash an OTA/RUU and make your phone subsequently unrootable.
However, there are some people who have downgraded their version of HBoot in order to get S-off with AlphaRev and have got into trouble when trying to flash the stock ROM back as it won't recognise the 'new' HBoot version. AlphaRev are working on this.