According to Zim's help file, you can, "If you have a larger number of pages that conform with the page description above, then close Zim, move these pages either into an existing subfolder to the other pages of the existing Zim Notebook folder or create a new subfolder inside the Zim Notebook folder. Reopen the Notebook and the pages and the new subfolder should appear. Rebuilding the index may take quite some time, if you have added many pages." I tried to import about 6.500 entries, and Zim seemed to choke on it. I wonder how many hours are needed for this.
Perhaps it cannot handle that many entries. nVALT does not seem to have this problem.