I frequently run 2 instances of the IDE to check examples but with a single Teensy connected.
Just to be clear, having 2 or more windows open is not necessarily multiple instances. You can use File > Open or File > Examples as many times as you like for lots of open windows, but they're all the same program instance.
Multiple instances means you run Arduino again. Windows Task Manager, Macos Activity Monitor or Linux "top" will show you have 2 complete copies of the software and Java environment running. With a single instance, when you change Tools > Boards or Tools > Ports, the change happens for every open window. People like Defragster working with 2+ boards tend to run 2 completely separate copies of Arduino, so they can have each with different board settings. If you have only 1 board, there's really no reason to run multiple instances. It uses a *lot* more memory on your computer. You're probably just opening multiple windows from the same instance, if you have only 1 board.
Would that still be a problem ?
Look, if I understood this bug well enough to answer this question with any confidence, I would know enough to fix it once and for all. Of course that is my plan, but as you can see from this conversation the bug only happens under pretty unusual circumstances and (so far) we don't even know exactly what to do to reproduce it.
Should you be afraid to try beta5? Definitely not! This bug is rare, it only happens if you have 2+ boards & instances of the software, and even then it is elusive. When it does strike, the problem isn't anything severe like crashing or losing data, but merely an annoying lag that can be solved by restarting the software.
If you do encounter this bug (which seems to have nearly zero chance since you're using only 1 board) or any other bug, please do take the time to post here with the details.
And a question for Paul - is it possible to separate Teensyduino directory structure from the Arduino one ? I'd like to have a single install of Arduino and multiple installations of the Teensyduino. Not urgent, but perhaps in the future (if even possible) ?
You certainly can have more than one copy of Arduino, each with a different Teensyduino install. If using Windows, you need to get the ZIP file download rather than the installer. Of course you also need to maintain some awareness of where you put each copy and which is which. Obvious as that sounds, it can be a challenge on Windows sometimes.
Just to confirm again, the Teensyduino installer only installs stuff into 1 specific copy of Arduino. On pre-10 Windows, it also installs an INF (or "driver") for hardware, but only the first time. Other than that hardware INF on Windows 8 & earlier, all the install happens only within the Arduino folder you select. You can have as many separate Arduino folders as you like, each with its own different copy of Teensyduino. I recommend naming they so you can easily see which is which, but if you need to check, just use Help > About (or Arduino > About if using Mac) to get the Arduino & Teensyduino version info for the copy you're actually running.
As far as the installation of files within a copy of Arduino goes, the answer is "it's complicated". While most of the stuff goes into Arduino's hardware/teensy and hardware/tools folders, the installer also has to touch a couple java jar files and many of the examples. These details can vary with different versions of Arduino, and they're likely to change in the future as Arduino continues to develop. That's why the installer carefully checks which version of Arduino you have. I don't recommend messing around with these internal details... but if you *really* want to dig into this stuff (taking a *lot* of time), the source code for the jar file modifications is on my github account, and all the other stuff is new or replaced ordinary files which you can detect by comparing an installer versus original copy. If using a Mac, of course you would use "Show Package Contents" to look inside. On Linux & Windows the Arduino software is just ordinary folders & files.