I had also issues with upgrades few times on php 7, then I started to follow one simple procedure ... 1.overwrite files with new one 2. switch back to php5.6 3. start upgrade process CLI or WEB(doesn't matter) 4. apply hotfix php7 and switch to php7 .
With this approach, I never had problems(today upgraded from 4.1.0 to 4.2 ) while uploading hotfix php 7 after overwriting and then starting upgrade throw up an error (...files encoded with 5.6...etc).Now I didn't go deeper into this issue since this approach works fine for me.