I created a backup for my site from ispconfig panel site/backup tab. site vhost file had reverse proxy lines in it. after I pressed save backup button vhost file became default state and reverse proxy lines dissapeared. is this a normal thing?
Yes. That is normal. Any site vhost files will always revert to default as per /conf/ folder upon settings being made or updated, so use /conf-custom/ if you are customizing all vhost file in your web server; or use chattr +i to avoid single site vhost from changes; or use a non ISPConfig vhost file naming convention for that single site. I never tested the last one but I think that should work too.
Yes, it's intended that ISPConfig managed config files that it's responsible for. Use the custom apache / nginx directives field on the options tab of the website to do customizations in a website, do not edit the generated vhost file manually.
I also want to ask php.ini customizations. do we have to add our customizations like; memory_limit = 512M post_max_size = 32M upload_max_filesize = 128M into webdomain/options Custom php.ini settings box?