We recommend that you perform a re-index, as configuration changes were made to 'Custom Fields'...
This is something we get a lot and we do try to re-index individual projects after every change to custom fields but
are there more that can cause the system to want to re-index? anything else that we do that demands the operation?
It's anything that might cause structural change to the index, so pretty much what Błażej just said. The index is almost purely about issue data, and most of that is field based, so the general theme is "messing with fields can cause it"
It is a little over-enthusiastic - a lot of add-ons don't really need it doing after installation or removal, but JIRA doesn't really have any way of knowing that. It's the same for some changes in field setup - you don't strictly need to re-index if a field is changed in some ways, but the code isn't quite clever enough and defaults.
Be aware though, deletes, field context changes and searcher changes may need a full re-index to get a clean index. (With a dirty index, like "you removed a field from project X, but only re-indexed Y", JIRA will work ok, but it's doing extra work to remove results from X before they mislead the user)
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