Michele, We encountered the same situation with our conversion project. We made the decision to include information about missing parts of a collection in the finding itself, including a note at the most appropriate level. The EAD tag library says that <scopecontent> may be used to describe "gaps" in a collection, and missing materials certainly are that. If an entire container (box) is missing, we usually note that information in a <scopecontent> nested within the main <scopecontent> and include a <head> that reads "Missing Material." We also note missing material at the appropriate component level, again using <scopecontent>.