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Question1..its not very important for me to change this before the next update,but will google index the new .htm when it crawls and penalize me for dupes?
Question2..Since all the new pages link to the .htm when google crawls again will it just drop the .html? or should I have to do a 301 permanent redirect to have google drop them?
Now let me ask you this: Why did you feel like you needed to change the extension of your URIs from html to htm? Just like you donīt change your name every other day it is a good idea to keep your URI namespace as static as possible. Changes in the filesystem namespace on your webserver should (almost) never cause you to changes the URIs as well.
Andreas