Thanks for your help so far @can.ozdemir.
We're currently using Kibana 7.9.3, I can see there are two upgrade paths available from the admin page (7.16.2 and 7.15.2), do you think upgrading might help?
Right now I think there is something fundamentally wrong, we have two other index patterns, both of which have mapping conflicts e.g.
These conflicts have been resolved a long time ago, but when I click refresh, no changes occur, I can see similar errors as above when I view the F12 developer mode e.g.:
GET https://8108e04d2b7a47a98da904a3323f33d4.australiaeast.azure.elastic-cloud.com:9243/api/index_patterns/_fields_for_wildcard?pattern=aqueduct-staging-*&meta_fields=_source 400
Uncaught (in promise) TypeError: Cannot read properties of undefined (reading 'get')
at IndexPattern.addError [as onError] (core.entry.js:84)
at data.plugin.js:14
When I click edit on one of these fields, I can see the reason for conflicts, but they are referring to index logs that have been cleaned up a long time ago (we only hold 14 days):
Anyway, this is the main reason why I started this thread because on our development index I was trying to fix the refresh issue, this lead me to delete the index and start again but now get stuck creating the index pattern 
The only thing I can think of, is to do an upgrade as I want to fix these mapping conflicts on existing index patterns and also re-create my dev index pattern.