@Technilamp wrote:
I did take a look at the model, it does however seem that there is a problem when editing the model,
Yep. When you put all that geometry into one sketch, you have no other choice but to select all of it to create the flange feature in the timeline. When I edited the sketch and deleted all the unneeded sketch geometry, the Flange tool now lacks most of the previously detected sketch profiles and works with cached geometry.


This is another reason why it is not recommended practice (in any modern parametric CAD software, including Inventor, SolidWorks, etc., to put all that stuff into one sketch and work with modeling features instead. I should have edited the flange feature to delete the previous profile selection and re-select it.
You engaged in another bad sketching (not drawing!) practice by working with a single sketch instead of breaking it into one sketch for the flange and one or more for all the features you want to add.
My model is not a workaround; it demonstrates recommended best practices for working with parametric, history, and feature-based CAD software.
My recommendation would be to overhaul your company guidelines and bring them in line with modern tools!
I have posted the model on the Autodesk Fusion Slack channel and it's been recorded as a defect.