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Blood Angels were able to get a tithe of recruits from all their successor chapters after being severely depleted. And as previously mentioned new chapters are usually given a command cadre from their parent chapter to guide them as they form.

Other than that I could see a very depleted chapter being folded into a parent or successor chapter in some circumstances. I don't think there are any examples in the fluff of that, but it does not seem unreasonable in some cases. Perhaps an Ultramarines successor that gets killed down to a couple squads left and being unable to rebuild might rejoin the UM.

Heres my big problem: what Chapter would you start in? With all the other Imperial institutions the difference between their sub-sections is mostly cosmetic (bar the various Ordos of the Inquisition, but since there are three main ones i'm thinking of having that as a trait selection like wow). some of the SM chapters are incredibly different to each other. what would your characters first chapter be? would it be the same for everyone? would they be able to switch chapters? if so how?

... 40k mmorpg is hard

I for one would avoid multiple moves as much as possible. It just doesn't swing with the Marines' oft-intoned fierce indepencence and unique Chapter cultures and internal cohesion, or the Imperium in general. That said, this is coming from a fluffnerd who has become very sceptical of MMOs dealing with established franchises because they have a tendency to bend and break the setting in much the same way, and I am of the firm opinion that things that cannot be portrayed appropriately should simply be left out entirely (this is a conviction I've developed during LARP, actually).

Here's a few ideas, though:

First you could move the player between his Companies. He starts out as a Scout, then moves on to, say, the 5th, then the 2nd, finally the 1st.

Then you could have the character move to another Chapter and explain this via some plot event. Maybe his original Chapter gets wiped out and the survivors decide to merge with one of their successors, or "fold back" into their parental Chapter. Alternatively, maybe that Chapter decided (a few years ago) to found a new successor Chapter there and then, and because the player character "and a few other selected Battle-Brothers" are so awesome they get chosen to help forming the new Chapter's core now that their brethren are ready for action.

Possibly rinse and repeat the Company stuff.

And for the last step, you could have the player character be selected to join the Deathwatch.

Have him rise from Battle-Brother to Terminator and lastly DW Captain.