The problem is that on my ubuntu 20.x server dists only python3 was installed but some of the code for indi-web
has #!/usr/bin/python scripts.
I made a link:
cd /usr/bin
sudo ln -s python3 python
Now indi-web reads and writes the correct configs .
This explains why it was working both locally and remotely when starting indiserver manually
but broke when using indi-web.