If you have many customization active they may very likely interfere and break your forum when you upgrade it to 4.0 or 4.1. There are specific instruction how to upgrade it in the right way.
But keep in mind that updating from vb3 to vb4 is a one way ticket and you might be not able to downgrade it after that. Also many of your mods and customization may stop work.
You may find these links useful:
https://www.vbulletin.com/forum/cont...rade-Procedure
https://www.vbulletin.com/forum/cont...to-vBulletin-4
And remember to backup everything first just in case.