It seems there is bug and sometimes file-indexing not triggered when adding/removing files.
I found that any change in the minidlna cfg file triggers indexing.
So as a workaround I do some change in the cfg file in Luci(miniDLNA) for examle from Standart to Browsable(next time vice versa) then Save-Apply and then restart miniDLNA from cmd line.
In general, I’d recommend to run every possible service (Samba, miniDLNA, git server) in LXC containers rather than on the Turris OS directly. You won’t be able to see service status in LuCI, but the advantage is to be able to get more recent SW and bugfixes available in the distro you choose to run in the container. Specifically for me, the case to migrate miniDLNA and Samba to containers some time ago was Midnight commander (mc) is missing UTF-8 support, but the benefits of isolating services in containers and getting richer user-space from the supported distros should be universal.