Two way street. You may agree to consent to a search of your vehicle as a condition of employment. If you refuse you are no longer employed. The employer has no right to destroy your personal property in searching after you withdraw your consent. You may use reasonable force to stop the destruction of your property. You must leave if required to do so, however, or be charged for trespassing. We went over a long thread on this one a while back, and I'm not budging from my position that personal property is personal property and that employment is a mutual agreement. If one or the other party withdraws from the agreement, it's no longer valid.
No 4th amendment prohibition applies, but just because my vehicle is on another's property (especially a parking area) gives them no right to damage it to satisfy their curiosity. In most jurisdictions this is called burglary of a motor vehicle and results in criminal penalties in addition to civil liability. Niceties of timing aside, if an employer asked to search my vehicle, he would get a "not in this lifetime" and if the issue were pressed, an immediate resignation or they could fire me. If they pressed the issue and tried to open my vehicle by force, I would use reasonable force to stop the burglary in progress and file a civil suit for damages as well as criminal charges. The employer has no more right to search your vehicle than a friend in whose driveway you may be parked while visiting their house. You are on the property with permission. When you no longer have permission, all they can do is ask you to leave and call law enforcement if you refuse to leave. You do not leave your rights at the door when you walk onto private property. Likewise, you have no right to your job if you choose to terminate the mutual agreement by refusing to allow the search.
You are always free to withdraw consent, subject to the terms of the agreement. There is no magical "continuing consent" that any party, private or government, can take advantage of. If you consent to a search of your vehicle by a law enforcement officer you may withdraw that consent at any time and he or she is required to halt the search. In this case, the penalty is that nothing found after you withdraw consent is admissible in court. If you withdraw your consent to search from an employer, he or she no longer has a right to continue and to do so constitutes a crime. Don't let anybody tell you any different. Stand up for your rights or you don't have any.