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If you have a lot of look up tables why not store them into a secondary memory location (like flash for example) and make sure that it does not get reset everytime you dump new software out onto the board (i.e. allocate the memory yourself).

Also what kind of times are we talking here, anything under a minute I would say is acceptible (anything more means you just need to be checking your work more and reducing the number of compiles like hardware developers do (I think you can guess what I do)).