Hi Lis,
I am not an expert in tvheadend but i am using "perl -pi -e" to update my muxes files as my ip providers changes passwords in url when my subscription expires and rather than scanning all channels again i just update connection url. I found solution on this forum using pipes and ffmpeg to my stability issues but at the same time how to use perl to update muxes files.
https://tvheadend.org/d/5282-iptv-buffering-stalls-general-drop-outs-settings-that-resolved-things-for-me
But in your case i am not sure if this applies as i removed my m3u file to prevent tvheadend scanning file with old urls.
In case you do try to update many files stop tvheadend service and backup directory so that you could revert back in case anything happens.
#backup
service tvheadend stop
cp -R /usr/local/etc/tvheadend/ /home/tvheadend/backup09012019
service tvheadend start
#restore
service tvheadend stop
#take a not of permissions assigned to tvheadend directory before deleting it using ls -l command
rm -R /usr/local/etc/tvheadend
cp -R /home/tvheadend/backup09012019 /usr/local/etc/tvheadend/
#run below command to apply permissions as noted earlier
chown -R tvheadend:tvheadend /usr/local/etc/tvheadend/
service tvheadend start