How to clean iMessage on iOS and redownload icloud data

Once a device is all enabled and synced up with Messages in iCloud, you can't delete stuff from the device without the risk of losing it from iCloud storage as well as any other in-sync devices and deleting stuff won't kick-start any syncing that's not happening or has not happened. One thing you could try, in order to kick-start syncing, without much if any risk is to simply disable it and give it time to download the stuff that had previously been offloaded from device storage to iCloud storage. This could be instantaneous for, if the device has plenty of available storage, the whole works could have been invisibly cached in temporary space. Otherwise it could take some time. Either way, it's definitely not done if a download progress bar appears in the app at the bottom of the conversations list. Then re-enable it. That might kick-start syncing. Either way, should be no harm done if you don't delete anything you need to keep.

I could tell you more but I'd need to know what the out-of-sync indications are so feel free to let me know. One thing's for sure. Messages in iCloud does not introduce any user-friendly, painless way to restore to a device anything that was deleted from that device after Messages in iCloud was originally enabled and all synced up.

You're not the only one to experience that problem. I think the easiest and safest way to deal with it is to manually weed out the "synced-out" residuals that remain on either but not both devices and go from there. On the other hand, if deletion syncing is consistently or continually not working, I'd temporarily disable Messages in iCloud on each device, one at a time. Don't do it on both simultaneously. You do this by toggling off Messages under APPS USING ICLOUD in iCloud settings. Give it plenty of time to download what had been offloaded from it to iCloud storage. Then later re-enable it and give it plenty of time to re-upload (re-offload from device storage to iCloud storage.) Then later repeat that cycle on the other device. If that doesn't fully retroactively re-merge the messages libraries of both devices, I don't know what would but it has been known to kick-start deletion syncing even if you nevertheless have to manually weed out the "synced-out" residuals that remain on either but not both devices.

By the way, disabling Messages in iCloud has no affect on new messages continuing to distribute across devices. My bad for spacing that out.