I'm not sure I see an issue with this running in Flow. Where do you see physical discontinuity? You can use the Gemoetry check tool to see if the geometry is okay to run. If I totally missed what you are saying, I appologize. You are welcome to try and explain in again if someone else doesn't help you out.
Thank you for the reply.
I think I should try to use the geometry check to evaluate if I will have a I problem, just like you suggested.
Can you provide some guidance on how I can use geometry check?
Go to Flow Simulation drop down menu, scroll down to Tools and choose Check geometry. Everything should be enabled by default, so just click Check.
Hope this helps!!
Geomtry check will tell you if your cavity is correctly closed so that Flow Sim can find a internal cavity (you may use lids to close it). If volume is 0, then your model is not properly closed.
It can also point out invalid contacts that need to be fixed. They prevent correct boolean operations.