yes raphael was always with rimuru in all of the other loops, but no, raphael doesn't have the knowledge about the time loops because rimuru himself is not aware of them. if I'm not mistaken, his great sage skill (now raphael) has 5 functions: hasten thought, analyze and assess, parallel operation, cast cancel, and all of creation, and all of creation is the one that allows raphael to know about everything, but the thing is that it can only know information that rimuru already knows about, like even if it's just a concept that rimuru has heard before and doesn't have much knowledge of it, raphael would be able to perfectly know what it is (as a skill)
but since rimuru is an outsider to chloe's experience of time loop, raphael doesn't know or have a memory of it whatsoever.

Did rimuru have Raphael in the past too? I wonder if Raphael actually know some of the past since she's always scheming behind the scene