Didi you update image or just autoupdate? Autoupdate will not delete these files if they exist. In fact extcommands.xml can only be read so server will never recreate it. With the image it will be replaced of course with the images default files.
Files can disappear from sd cards due to errors in file system. Seems to happen more often on sd cards then on real drives. So make sure to always shutdown before removing power to reduce the risk at least.
I made an update from running system and the files where defenitely gone!! i put in my backup files and it worked again. Updating to 0.93.0 was without any problem. By the way I'm using SSD's on my Pi's since a long time, because of wanting a more stable system.
Good to hear that it did not happen again. Our installer do not contain that file and we definitvely do not delete it, so no idea what happened here. That file is also only read - we have no write function for safety.
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Files can disappear from sd cards due to errors in file system. Seems to happen more often on sd cards then on real drives. So make sure to always shutdown before removing power to reduce the risk at least.