The SCI index includes journal titles and has nothing to do with individual issues. If a journal is indexed in SCI, all its issues will automatically be covered under this. Moreover, special issues are always based on more important topics. Therefore, there is no reason to exclude special issues from the main journal. You need not worry; if the journal continues to be listed in the SCI database in 2016, your article will definitely be listed. If your article has the right keywords and they match the keywords for the journal's special issue, the published article will be easily retrievable in online searches.
However, if you still have doubts about this, you can write to the editor. I don’t think the editor will be annoyed if you have genuine questions. However, make sure that your email is brief and to the point and avoid unnecessary questions as far as possible.