[importsjc]

Ok, after doing testing I have narrowed down the timer reset to the line

timer.start();

here is some test code that is resetting when you start and then stop.

/*
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package Custom;
import edu.wpi.first.wpilibj.Timer;

/**
 *
 * @author Robotics
 */
public class TimerTest {
	Timer autoTimer;
    public void robotInit(){
        
    }
       
    public void autonomousInit(){
    	autoTimer = new Timer();
        autoTimer.start();
    }
    public void autonomousPeriodic() {
    	System.out.println("AutoTimer First: " + autoTimer.get());
    	Timer.delay(2);
    	System.out.println("AutoTimer Second: " + autoTimer.get()+"\n\n");
    	autoTimer.stop();
    	Timer.delay(2);
    	System.out.println("AutoTimer Third: " + autoTimer.get()+"\n\n");
    	Timer.delay(2);
    	autoTimer.start();
    	System.out.println("AutoTimer Fourth: " + autoTimer.get()+"\n\n");
    }
    
    public void teleopInit(){
    }
    
    public void teleopPeriodic() {
    }
    
    public void testInit(){
    }
    
    public void testPeriodic() {
    }
    
    
    public void disabledInit(){
    }
    
}

you should notice that after the timer is re-started the autoTimer.get(); printout becomes 0.

I have actually solved my problem using an offshoot of what @legts suggested.

Thanks for the help!