I chatted with Apple support about this issue. Unless you have a backup stored, the data is gone.
Here was the conversation:
Me: Hello, all the guides I have created in Apple Maps are gone. I am connected to a network, have the 16.4.1 iOS update, and location is turned on for maps in Privacy settings. Please advise how I can get my guides back.
Apple: How long has this issue been occuring? And when did it first start?
Me: It happened after I installed the latest update, within the past month. I thought perhaps my phone wasn’t connected to the internet, so I restarted and forgot about it until today. After checking online forums, it looks like many people are having the same issue, but I haven’t been able to find a solution.
Apple: Does maps show as listed under your iCloud storage?
Me: Yes
Apple: Being that this is app data you would have to recover and restore your device from a backup to enable these settings again ok?
Me: Is there any other way to retrieve this data? I do not have iCloud backups on
Apple: No this would have been the only possible way to retrieve this data as it is stored in an App, ok?