Just to update this, I wrote a custom ReadImportTag function for this block, performed the upgrade again, and the company info is there. I then exported CYBlock from the new version and the export tag is correct i.e. cyblock2.
I also updated a sample data system from and to the same versions but the problem did not occur.
Another partner has had issues with a block being empty after upgrading, but it was APAccBlock. I don't know if this is related.