Whew, am I frustrated, brace yourselves.
I once again have run into a toolpath changing problem with Fusion360 and have no clue what is going on. My biggest problem is explaining the issue to other people as I can't replicate the issue, and there is no "issue" per se.
Talking it out with my father, he helped me see a bit more of the problem and where it's occurring. In a very basic example, say you have a square shape, and you want your endmill to follow half the outline of the square to cut it out, so starting in one corner, you have it trace the outside and stops at the opposite corner. This works fine, and you get the machine to run it.
However, say you change your mind and want the tool to run past the final corner and keep going half an inch longer. You make that change and nothing else and re-export the code. When you run this new program, it goes the extra half-inch, but now it cuts the corners leaving little chamfers, which you didn't input into the program. Technically, if you go back and look at the settings, you can see nothing wrong, and the program is doing exactly what you told it to. The machine didn't crash, the toolpath ran exactly like it was supposed to. But your final outcome was not, because now you have a square with rounded corners.
My boss thinks there is some issue with the software where it's making changes to 'set' toolpaths, which technically I suppose it is because I am making a change to that toolpath. But I didn't tell the machine to round those corners off, but it did it anyway, and if I simulate it, I can clearly see that it rounds the corners off.
My only idea as to the cause of this issue is over constraint.
Fusion360 likes to be "automatic" and will have preset values for you when you select toolpaths, which are great. However, those values read off of each other, which is where it gets complicated. Say you have a parameter in the setting of the above example, saying that it will make square corners as long as it is within one inch of travel distance, but anything above that will shave the corners off. Now your first toolpath works fine because it's within an inch, but if I wanted that extra half-inch, then it would push it outside the limit and turn on the corner-cutting setting.
The problem arises when I set up my initial operation, and I inevitably need to change something, so I go back and change it for the next run. Then I run through the new program, thinking it will only make that one change. However, that change may cause another effect, in essence turning on the 'corner-cutting setting.' It's not the fault of the software, but rather how it was setup. If I were forced to input every single parameter and setting into each toolpath, I would not have a problem, but that would take huge amounts of time when you get into more hairy 5 axis projects when you have 50+ toolpaths. So you have to have some preset information to make the workload possible.
If there is a way to turn off all presets in Fusion360 and leaving them blank so that I would be forced to fill them in before generating the toolpath, I feel that it would solve this problem. Unfortunately, I'm not sure if this is possible or not and will have to do more research. The most frustrating thing about this is that I can't seem to find anyone who really understands this problem or has faced it.