Another update. I did the following and got it working on a Windows server:
So here's an update after a week of Support Rotation in London. yannK and you provided me with the fix, although we do not really know the exact reason we hit the issue.
On the indexers I added this to limits.conf and restarted:
[lookup]
max_memtable_bytes = 100000000
This fixed it! However as a general best practice I also added the following
distsearch.conf on the search head to fix a general Windows (checksum?) issue:
[replicationSettings]
allowDeltaUpload = false
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