Get the Imperial Assault Campaign module for Vassal from http://www.vassalengine.org/wiki/Module:Star_Wars:_Imperial_Assault
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So, i am pretty confident they can keep their heroes at the status they are at the end of the SWIA base campaign, since Twin Shadows is designed to be inserted into a bigger campaign anyway.
The minicampaign is not designed to be inserted into a full campaign. The minicampaign consists of missions that can also be used in a full campaign as side missions (and agenda side missions).
Story mission balance will be quite out of whack if you go into the campaign with fully developed heroes. (Side missions less so.) The threat level and initial groups for each story mission have been selected for certain power level in mind.
However, the minicampaigns start with 3 XP and a wad of credits, so the heroes do not need to start from zero.