I'm currently running the official nightly of cm12.1 on my LG G3 AT&T (model d850) with the Xposed Framework installed. However, every time I manual update Cyanogenmod (as I don't have a compatible recovery for automatic installation), the Xposed Framework gets removed/disabled, forcing me to locate the downloaded framework zip file (xposed manual installation because of reasons). This is not really a big issue for me and doesn't greatly affect myself or my phone in anyway but it will be glad if someone has found a 'possible' solution for this minor bug
Ok so this isn't a bug but in the updater script of the xposed framework, a function called install_overwrite is called upon several occasion and, hence the name overwrite, will replace pre-existing file in the /system folder. So in order to install the xposed framework, it's necessary to reinstall it with each update.
This script will automatically reinstall Xposed after dirty-flashing a ROM (i.e. flashing it without wiping userdata). The linked post includes instructions to download and how to install it, and describes how it works. https://www.reddit.com/r/xposed/comments/3u2xw9/release_xposed_addond_backup_scripts_it_keeps/
Try to search "xposed script after updating cyanogenmod" with your search engine