Nope.
Your Aces High configuration won't care - it doesn't even know that it's USB, let alone what port it's plugged into or been plugged into. All it is to AH is a Windows device.
There is of course at least one caveat - While AH isn't going to care, and Windows itself (generally) is going to key off of a unique device identifier and "connect" it to the same device representation in "hardware" regardless of what port it's on - some of the manufacturer supplied support software is more than a little squirrelly and you may or may not have trouble as a result if you are using that.
But generally, no. However, post back what type of controllers you're using, and if you use any manufacturer provided profiler/control softare, what version and someone with that samd combination can tell you for certain if they've had issues.
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