Search Api - added fields disappeared from Fields list

Huh. That's really strange, yes … Did you have any of the fields of the field collection that vanished marked as "Indexed" already when it vanished? Normally, those should never vanish, so that could be a workaround: after adding the related fields of a certain field collection, mark all desired fields of that collection as "Indexed" before proceeding to add other related fields.

If you press "Save" it is expected behavior that those related fields for which you didn't mark any properties as "Indexed" will vanish again – maybe suboptimal, UX-wise, but currently how it works. (Was changed already in D8, though.) Was that maybe the problem?

Just a note on a similar problem that I was facing: adding a related field and clicking "Add fields" was doing nothing - the field list that loaded afterwards was the same as before, no trace of the new field. The problem for me is that this site has a pretty big list already being displayed (654 rows), which means more than 1000 input vars for PHP; the solution was to increase max_input_vars to 10000 in php.ini (only in the local/development server, this doesn't affect a production site unless the list is being updated there).

Hope it helps.

@jedihe That helped! However, I still wouldn't see the changes reflected on the form, until a I cleared all cache.

OK, then seems this is fixed?
Thanks for reporting back, in any case!

Yes, I had the same problems of index fields suddenly disappearing, and max_input_vars was the probable cause, because now it seems to work well.