What to do if a colleague plans to submit the paper you worked on together without your name on it?
I have been working with another postdoc on a paper, here is what happened: I presented a work of mine before it was published (but it is in my thesis and on arxiv) and he decided he will use the same exact model with a slight change


There is a misunderstanding about "publishing": you probably mean that it was not published in a journal/conference, but apparently you did publish your model, which means two things:


Your authorship on this is established
Anybody can reuse it, provided they cite your work appropriately



  The methodology belongs to me


Not really: yes you are the established author of the methodology, but it is now available for anyone to reuse it, as per the usual academic process (the only exception would be if you patented the work prior to publication).


  I have talked it out with him and finally with my lab adviser as he was not collaborating, and we decided to send the paper as coauthors after our adviser mediated the issue (though it was bumpy), even sorted out whose name goes first etc. 


This is what gives you a (moral) right to be a co-author for this particular work.


  My advisor has asked their collaborating institute whether I could join (the irony that my methodology is stolen but I need a pass to join the project) and they did approve it (I have all exchanges and emails)


Avoid using the word "steal" if you published it: if all that the other author did was reading your thesis/paper, the only requirement is for him to cite the origin of the work.


  I also suspect that my adviser got the patent of the code on his name as I have noticed he took my name out of contacts on github recently. 


Are you talking about an actual patent? If yes, for what? If this is about your methodology which is already published or about a code publicly available on github (under a particular license maybe?), it's unlikely that a patent would be granted, but IANAL. 


  Today I get no reply from him on multiple attempts and I learnt that he has removed his computer's hard drive and my adviser is off for vacation for an unknown time


Multiple attempts over how long? If it's only a few days there's no reason to panic, he might be busy. Did you agree on a method to write the paper together, a venue to submit it or a deadline?


  I suspect that my colleague will try to send off the paper we were supposed to write together without my name on it, I have email exchanges as proof but most relied on my adviser, whom I don't know if I should trust after the copyright issue. What do I do if he sends the paper without my name? Do I write to the editors? His partner institution? Is there a board for this?


You should rely primarily on your advisor, and if they don't cooperate you should seek support in your institution, e.g. head of department or ombudsman.