SolidWorks Pack and Go for not messing up references

To access Pack and Go:
In SOLIDWORKS, click File > Pack and Go.
In Windows Explorer or SOLIDWORKS Task Pane File Explorer, right-click a SOLIDWORKS document and select SOLIDWORKS > Pack and Go .
In SOLIDWORKS Explorer, select a SOLIDWORKS document and choose SOLIDWORKS Pack and Go .

Files that are embedded (Design Journal, for example) are part of the document and are included without being listed in the Pack and Go dialog box.
source: http://help.solidworks.com/2017/english/solidworks/pdmworks/c_pack_go_ovw_wpdm.htm