I’m having this issue too. It stopped going back into the recently deleted folder for a few days after the IOS 18 update but now it’s started back again and I only have 3 days left before it permanently deletes!!! For some reason when I reset my settings on my iPhone the latest time (I’ve done this over 5 times) it recovered all messages I’ve deleted including the one that keeps auto deleting everyday. I have called apple and spoke to so many agents none of which have a clue how to fix this. The last person I spoke to was a senior advisor who said if the problem persists they will have an engineer look at it.
I have done so much troubleshooting i.e, factory reset, resetting all settings on my iPhone, logging in and out of my Apple ID, turning iMessage off an on. None of it has worked. I have an iPhone 15 pro and just like everyone it’s only one contacts thread that keeps getting deleted. Another thing I noticed is it only goes into the recently deleted folder every time my phone syncs the messages to iCloud which is odd.
Apple needs to have a solution for this asap otherwise what is the point in having a recovered option if your messages just keep deleting!