Ok lets start from scratch - Boolean modifier with fluid...

I had difficulties with the video before (and a poor explanation), it should be worked out now:

I want the cylinder on the right to be filled with liquid (left cylinder would be empty), then, as it reaches the the other cylinder and forms a new merged “container” I want the fluid to flow into the new empty space. I was trying too do this with a boolean modifier, but the fluid would just stay contained in the first cylinder, and never flow to other container once they were joined, despite the fact there was no longer a surface to contain it.

Any ideas for me?

Sounds like you need to use a control object.

Any chance you can elaborate? I’ve messed with fluid controls a bit, but I’m not quite seeing how it would achieve my goals here…

Apply the boolean to the control object, not the domain. Then the fluid should flow around the hole.