While opening old ChemDraw documents, I found multiple bonds present in my structures disappeared

Make sure you have the correct Bond spacing. You can check the settings in the following way:

1. Open the Documents Settings dialog from the ChemDraw File menu.
2. Go to the “Drawing” tab.
3. Select the "Spacing" option and change it to “% of length” with a bond spacing of “12”.  Deselect the "absolute" (-0 in) if that option has already been selected.
   
4. Then click the OK button, and you will get the following warning dialog.
5. Click the Modify existing button to override the old setting present in your old documents.