Planning Consolidated Reporting Line Item Summary

When I run the Consolidated Reporting Line Item Summary it includes closed projects, not desirable.  Also, it doesn't include some projects, I believe, because there are too many.  I have to manually choose half of the projects to run "part A" and then the other half "part B" for the remaining. This is time consuming.  I believe this happens because of the 9999 PENDING TRANSACTIONS LINE ITEM always being Active without the ability to close it.  Is there a solution?  I have spoken to someone on chat, but it could not be resolved.