Helicon Focus 9.0.1

[Catherine]

when I retouch the image, the reference window on the left suddenly becomes darker (see attached image), and this effect is random.

Thanks for the screenshot, we're looking into this. There's probably a specific combination of factors that triggers it, which makes it hard for us to reproduce the issue.

Would it be possible to add an option (within the Substacking section of the source image settings) to substack using one method (e.g. Method B) and then render the full stack across all the sub-stacks using a different method (e.g. Method C)?

Sounds good, we'll add more controls to the substacking tool so you can select different methods.