iCloud notes disappeared?

Recently I moved my ‘On My iPhone’ notes to iCloud. I have about 4000 of them and when I moved them everything was fine and they all came up in the iCloud folder, although they were only taking up about 90Mb of storage (when they were in the ‘On My iPhone’ folder, they took up about 700Mb). I then turned notes off in iCloud settings because I didn’t need access to them at that time. When I went to turn iCloud notes back on later, only about 300 notes came through from the cloud. This wasn’t an issue as I was able to restore from a backup and get them back on my phone, but if I were to do this again in the future, how would I make sure they all came through?