Others have said, while in SM, remove weapons computers not cannons themselves. Also any docking modules, docking enhancer blocks are fine to leave, they can be re-linked later.
K10wN:
Once I deleted the weapons, salvage, and missile computers from the ship, the file will open up in SMEdit like normal.
Reconnecting the weapons again ingame is quick with shift+v, which will connect all the blocks in a group in one click.
Once done removing those blocks, and still in in core, build mode, hit the return key to enter chat. use \"/save yourshipname\". This will update the blueprint, just incase your ship is gone next time you login. Always save!
Then go back to SMEdit and use the OPEN menu to open the in-game ship, or blueprint. I like to edit in-game, so it will just be updated next time i login to SM. No need to \"/load yourshipname\" back in.
hope that helps.