I have a list of 60k+ records and I am needing to move them into folders to keep the list views lower than 5000k so we can stay under the List view thresholds. I had created my folders using an append query in Microsoft Access. I named the folders year-weeknum (i.e. 2018-26, 2018-27 etc). I then used the site content and structure tool to move the items into their folders. After moving the majority of them my business areas started reporting that some of the fields were blank and that the version history was lost. I then created a new list on another site collection to test the move feature to ensure I wasn't losing data. I specifically tried multi valued fields and a multi-text field with appended comments. In my tests the items moved without issue and all data was intact. For the life of me I can not figure out why I am losing the data in the Production list. All sites are in the same environment.
Instead of folders, you can set up indexed fields, which will also avoid list view threshold issues. Though, some list-wide operations, such as changing permissions inheritance, will not work with lists that have > 5000 items, regardless of whether folders are used or not. If you're on-prem , these sorts of issues can easily be dealt with by having admins set up certain times where the list view threshold isn't applied, when you can do those sorts of admin tasks. Online, options are more limited, and the usual route is to use a 3rd party tool to move list items out and then back in. But regardless, I'd configure indexed fields before moving things into folders and breaking everyone's links.