E-Tube Project Professional won't work with my charger. I don't own SM-PCE02!
With the announcement of the new DURA-ACE R9200 and Ultegra R8100 groupsets, Shimano launched a new E-Tube Project version - "Professional".
If you have an SM-PCE02 then, by all means, use E-Tube Project Professional.
E-Tube Project V5 / Professional states:
Connect SM-PCE02. Connection can be made with all the units that compose the bicycle or with a single unit only.
This software is not compatible with the SM-BCR2. Please connect a compatible PC linkage device
I recommend using 3.4.5 if you're using the SM-BCR2 and using 4.0.4 if you have an SM-PCE1. Of course, you can use 4.0.4 with the SM-BCR2, but keep in mind that you may need to use the older E-Tube Project version to update the charger before it'll work with version 4.0.4. You can find versions 3.4.5 and 4.0.4 on the E-Tube Project Archive page.