The settings should never be deleted or overwritten by our setup assuming you are not switching between Release and Beta and/or not installing in a different folder as the previous version. In fact for quite a few versions all your settings should be kept - no matter what.
Any chance what you're seeing is installation folder related?
I don't think so. I let the update install itself 'automatically' and let the software select where it installs itself and what it deletes from the prior one.
Sorry that took so long (30+ minutes), but I just went through the upgrade from 11.11.5 to 12.12.0 on one of my three machines. (XP pro, SP3, 1.86 GHz, 1Gb) using a serial port to drive the Key-Com cable. I let the upgrade take place 'automatically' with the software choosing file names and paths, letting it delete and extract files on its own until it, as customary in my experiences with every upgrade, produced the expected "First Use, No Config File Found" message forcing me to, once again, teach it to use the same port every prior version has used.