We have some indexes that have suddenly stopped indexing the custom fields we had configured on our logs.
There were some changes made to create a new deployment app at the time the problem started occurring, however I have still been unable to track down the cause of the issue. Can anyone assist in pointing me towards which config files I should be checking? Are there any troubleshooting tools that can assist?
Do you mean this issue has occurred since you created new App? If so, new App setting seems to affect the issue.
I guest your New App permission affect the old App. Could you check it by looking at the manager-> app -> sharing permissions? If new App is "global" setting, it means it affect others.