When I open an existing document, the bond crossing (front to back ordering) is not preserved.
This problem does not occur in the latest version of ChemDraw.
In 6.0, this would manifest in the following circumstances:
1) The structure had non-default bond crossings (two bonds crossed, and someone changed the front to back ordering by doing a Bring To Front/Send To Back)
2) The structure contained at least one non-atomic nickname (CH3 is atomic, Me is not, CH2CH3 is not)
3) At least one non-atomic nickname was created after the last time the document was loaded from disk.
Draw two bonds that cross
Select the back bond
Choose Bring To Front
Label the end of one bond Me
-->The bond crossing has changed
BUT NOW CONTINUE THE RECIPE:
Put the bond crossing back to its desired ordering
-->The bond crossing has been preserved correctly.
The difference between the first and the second is that the atom label was created after the open in the first case, but was already existing after the open in the second case.
Note that you really have to close and reopen the document to get the ordering to “stick” properly. So, copying and pasting a modified document would always cause the problem, but copying and pasting *after* saving and reopening the document would not.