A flight plan allows the submission of up to two alternates (item 16). I would suggest that if, for whatever reason, at the planning stage you don't intend to make use of the one or two that have been named it would be prudent to submit a modified plan - if only for the com failure plus diversion scenario mentioned above. I believe that a supplementary flight plan (SPL) message can be used for this, so not a re-file as such.