I was thinking in starting an adventure with my group who plays mostly fantasy, my idea was to sort of trick them into playing a new system on a world of sword and sorcery and at the end of the first adventure would be the astartes coming down from the sky to recruit warriors and do one shot adventures with them climbing through the ranks of the chapter beginning as scouts then tacticals and so on until they a recruited to the deathwatch with long downtime periods where they learn behind the scenes more about the universe and decades pass.

I'm sure someone must have done this or something similar before, any tips?

@ Alagard ...

They already have officially hybridized between WFB and WH40K... WarHammer: Age of Sigmar.

While this is for the miniatures gaming, the themes and story-premise(s) can be (and essentially have been) easily blended.

I was thinking more on rules tips, progression, abilities that can be used while not being astartes, etc. my plan is to tell them we are playing something like dark sun in the old D&D setting with this new system, I want to keep the real game system and gameplay hidden from them for a few sessions so that the players feel the same amazement as the characters when the astartes come to recruit them, I will hint that they are giant gods in imprenetable armor that come down of the heavens once every generation to take the bravest of warriors to fight alongside them

Well unfortunately the WH-F(antasy) RPG is wholly different than the WH40K RPGs, so no integrate-able love there, if you are trying to preserve the rules systems between RolePlay settings so your players can feel comfortable playing within the same rules system rather than having to jump to a different rules system upon realizing they have gone from WH-F to WH40K.

In terms of comparative power-levels, per WH40K RPGs, from lowest to highest...

1. Dark Heresy (Acolytes)

2. Only War

3. Rogue Trader ~ XP-wise, this is where Rogue Trader ranks for power-levels. RolePlay-wise, Rogue Traders are ranked as equals ("peers of the Imperium") to Inquisitors and Space Marine Chapter Masters.

4. Black Crusade (included for completeness)

5. Dark Heresy: Ascension (Inquisitors & Throne Agents)

6. Deathwatch

One possibility is to use Dark Heresy &/or Only War rules and power-levels, but restrict to Feral &/or Feudal World classes and gear, and psyker rules for "magic".

There is also the contradicting lore of Space Marine recruitment. Are you recruiting your Players when they are kids (young teenagers) as traditional Space Marine lore dictates? Or are you going with something more akin to WH:AoSigmar for noble warriors taken at the height of their native power?

I was thinking teenagers (15/16 yo), I dont have those books, which one would you recommend, dark heresy or only war? feudal world clases with pskyker as magic sound interesting

There is very little difference for XP power-levels between Dark Heresy and Only War.

In terms of Rank-1 starting XP levels...

1. Dark Heresy starts at 400 XP. Acolytes are the scrubs of the Inquisition's forces, expendable, unrewarded, and unlamented.

2. Only War starts at 600 XP. The cannon fodder of the Imperium's ground forces, aka The Imperial Guard.

3. Rogue Trader starts at 4,500 XP.

4. Black Crusade starts at 7,000 XP.

5. Dark Heresy: Ascension starts at 13,000 XP.

6. Deathwatch starts at 14,000 XP.

Book-content-wise, I cannot really make an accurate comparison between Dark Heresy vs. Only War. I have Dark Heresy books, but I do not own any Only War books, as I foresaw that it would not be a popular series and thus not worthwhile to invest in.