Apparently it should not cause any problem. Just redeploy them!!
But it didn't work. The error message was quite clear, one of the dll ( name unchanged) is still being referenced by some of the old library( name changed). And as they are not in the current deployment list anymore, Visual studio is not un-installing them automatically.
What should I do. Just thought why not just drag them out of the GAC. So simple.!!
Now as the related BizTalk application still referring old assemblies, it can't delete the application, because it can't find required dlls in GAC.
How to fix it now???!!
Why not just dive into BizTalk database and delete those application configuration information. Did that !!! So stupid!!!
I'm not a guru of BizTalk internal database obvious reason i messed up the database. And you know what I had to reinstall the whole dam BizTalk[ my dev machine only :) ] again. Amy be I could have only reconfigure it. But that thought never cam in my mind in the first place.
So the moral of the story is, don't play around with assemblies in GAC use proper tools to do the job. :)
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