Just wanted to update here (And also feel like I owe @Punka an update 
) - we solved the issue by reducing the limit of the schema query (using DATABASE_SCHEMA_QUERY_LIMIT var)
Seem to be caused by the number of schemas we have in our DB, and the fact that querying information schema is not always a best practice and not a very efficient process.
The query took too long and it caused the db-connector to die, not before killing the server (after increasing the server resources the connector died without killing it and then we could debug the issue a bit better)
Thanks again @Punka !