Merging blockchains after algorithm change
That seems possible, but I'm not aware of any instances of it being done before.

You have three major problems:


Bitcoin generally assumes that there is one single ordering of transactions. That ordering can change, but there's always only one. The danger is that your two blockchains contain transactions that are mutually exclusive: transaction A and transaction B both spend the same coins, so only one can exist in the new master chain.
Everyone needs to upgrade to a client that supports the new merged blockchain, and the algorithms in both chains. Some people might have been screwed over by the previous step in the process (because a transaction they relied upon was essentially reversed,) so they might be a little reluctant to do this.
You need to avoid introducing any subtle security bugs while doing this.