If you created a constraint ( CREATE CONSTRAINT [see details here]) or index ( CREATE INDEX [see details here]) on nodes or relationships (or legacy fulltext index via  db.index.fulltext.createNodeIndex or db.index.fulltext.createRelationshipIndex) and subsequently receive an error stating the index or constraint is missing when running a Cypher query or any API call that would rely on that index / constraint, please check the following:

• Check that the index or constraint was successfully created with SHOW INDEXES (see details here) 
• Review the log file query.log for any index or constraint DROP (DROP INDEX, DROP CONTSTRAINT)
• Review your queries and check any calls to CALL apoc.schema.assert(...).
  The default behavior is that when calling:
  apoc.schema.assert({indexLabel:[indexKeys],…​},{constraintLabel:[constraintKeys],…​}, dropExisting : true) yield label, key, unique, action
  the last parameter dropExisting is by default true and therefore the schema is replaced.
  See further details here.
• Check that no database dump or database export has been loaded that would overwrite the existing "schema".

If you tried everything above, regularly poll on SHOW INDEXES and log the output to a debug file in order to narrow down the time interval of the issue and review the queries or events.