This morning I was woking on my guest OS (windows 7) with USB-Serial board and it was working just fine. After the upgrade to Parallels11, my USB-serial board is not recognised in guest OS anymore. I get yellow exclamation mark icon and COM address is not assigned. Nothing else was changed on the guest or host system, except the Parallels upgrade. My host is Yosemite and guest is Win7.
This is much more likely to be a Windows driver issue - the latest Windows driver does not work with fake (Chinese) PL-2303 chips. I would hazard a guess that the new driver was installed when you rebooted. Try rolling it back to the previous driver.
I've binned my old (assumed Genuine) Prolific USB converter. FTDI also tried this game, but what they should realise is I will never purchase another Prolific converter - Fake or genuine! These chips are often included in other products as well!
I, too, am having problems, but it appears to be due to using a USB hub. I have 3 FTDI serial-USB converter cables, plus an Asus Xonar U5 sound "card" going into a Sabrent-branded USB hub that uses the same chip as the USB hub built into my early 2015 13" rMBP. After the "upgrade" to El Capitan and Parallels 11, Windows 7 Home Premium can no longer see those devices, but will see one of them if it's plugged directly into the rMBP's USB port. I've filed a support request with Parallels, and we're working through it, trying various settings, etc., and I'm hopeful that there will be a resolution. (It worked properly under Parallels 10 and Yosemite, and the hardware has been verified as working correctly using various apps that run directly under El Capitan). Yes, I went to the FTDI web site and obtained the latest drivers from July, 2015, and also the Renesys drivers from Intel for the hub. It's worth noting, though, that several other software vendors have had issues with El Capitan, and according to an article that just appeared today in 'OS X Daily', Apple apparently changed the security model/structure in El Capitan, and I've also seen mention/discussions in other forums that they may've also changed the USB stack. One application vendor (which doesn't talk to hardware) indicated that they had had to change their compilation environment several times (new versions of Xcode and GCC/whatever) to produce running code for El Capitan, and there are still some problems they need to resolve, even though they didn't change any functionality. (I have NOT tried disabling the System Integrity Protection, as described in that article, nor do I necessarily recommend that anyone do so, unless in a closed/protected "clean room" environment). So, in my personal opinion, I suspect that Parallels is possibly the victim here, not the villain.