1 . goto beyond compare folder

 cd "/Applications/Beyond Compare.app/Contents/MacOS/"

2 . rename BCompare to BCompare.real

 mv BCompare BCompare.real

3 . new a file named BCompare

 touch BCompare

4 . write following code into BCompare

#! /bin/bash
if [ -f $HOME/Library/Application\ Support/Beyond\ Compare/registry.dat ]
then
    rm $HOME/Library/Application\ Support/Beyond\ Compare/registry.dat
fi
"/Applications/Beyond Compare.app/Contents/MacOS/BCompare.real" &

5 . make BCompare executable.

chmod +x BCompare

refer to: beyond-compare-4-for-mac-unlimited