I feel I did a poor job of explaining the problems I had yesterday.
For some of the more complex milling operations with many toolpaths in them, I've had some weird issues when I change one of the toolpaths. I can't put my finger on where the problem is coming from exactly, and there's no way of quite defining it.
As I am putting together a large operation and I find I need to make a change to one of the initial toolpaths or model itself, it almost always causes something to change with the other parameters in the toolpaths that I've set up. The problems are never major and are almost always an easy fix, but most of the time, I don't catch it until it's too late. This has always been an issue since I got started using Fusion360 and became more prevalent in the complicated setups.
For example, I could get one of the contouring toolpaths to leave a very nice surface finish, but later, when making changes to toolpaths behind it, I come back and find that it's now faceted. None of the settings have changed in the process, but there always seems to be some small deviation from the original toolpath.
This isn't really an issue if you don't make any changes to your initial setup, but in my case, I have to play around and learn how to find the best machining methods, so I have a lot of small edits throughout the process.
Thinking through the problem and talking it over with my boss, I think the problem traces back to Fusion360's linking setup, where the initial operation setup wants to link everything to the 3D model you're basing it off of. In contrast with Mastercam, which creates each toolpath independently from one another. In speed runs that don't require a lot of tweaking, Fusion is definitely superior, but making many small changes makes it more beneficial to have toolpaths not connected.
One solution I'm working on today is breaking the 3D model down into surface planes instead of a solid model. This will allow me to create each toolpath independent of one another and make it easier for isolated changes. I'm also using a few new tips I got from my boss when it comes to sketching geometry, and I'm relying more on that than the hard boundaries of the 3D model itself. It's a bit of an outside box programming method, but I'm finding it's actually quite faster to do it this way. The downside to this method is that if any changes are made to the 3D model, everything must be updated manually, which isn't a problem as the geometry is fixed in contract jobs.