Transplant risk from Ebb&Flow to Autopot in second week of flower

[mare73]

I am currently in second week of flowering. As you can see from the pics I have a DIY Ebb & Flow system with two plants that grow in rockwool/clay pellets. I am used changing nutrients and cleaning my tank every week and after a month of growing in this system it has become really difficult to manage ph values, nutrient values and everything else because the access to the tank is only possible if I raise the growing container. Not only it is heavy but with plants growing it is also difficult to move it. I already have an Autopot system waiting for the next grow but I am really thinking of transplanting this two ladies to their new home because only the thought of managing this sytem for 2 months or more makes me nervous.
I think I can dig a little, remove some pellets and get them out without risking too much for the roots and place them in the new pots.The only problem could be if the roots of the plants are tangled. What do you think?
The first picture is from a month ago, the second was taken 2 days ago.