I just upgraded to an official(?) 1.49.0007
Before the upgrade I changed my CID to HTC__001 (I thought it's not possible with locked bootloader but it worked, my CID was HTC11111 before)
I used this zip file: downloadandroidrom dot com/file/HTCEvo3D/hbootdowngrade/Free%203VO_V2.zip there is a rom.zip file inside, just renamed that to PG86IMG.zip and put it in the root of my SD. It upgraded me to 1.49.0007 and after i just simply used Revolutionary to go S-off.
I hope this helps if someone finds an EVO 3D under a rock which still has HBOOT 1.48.0005 and wants to go S-off.
And thanks for the answer, I'm not sure if you suggested something like this, or to go to the newest HBOOT and downgrade from there, but I was trying to keep things simple.