Unreconciled transactions and investments transactions won't be cleared out. Most of the users here recommend you just hide the accounts. Just make frequent backups.
You can do a year-end copy but most of us here don't recommend it. It's better to leave all your data and history together in one file and it should not affect performance. Sometime in the future we guarantee you will want to see something and you won't be able to merge them back together. You can run reports for any time period. Just copy your whole file for a backup (which you should be doing regularly anyway) and continue on in your current file. Too many times people ask for help on how to re-merge their data, which can't be done. Also any uncleared checks will then show up in both files. So just continue on. And if you upgrade to a newer version in the future you will have to remember to convert all your old files too.
Or you can do a File - File Operations - File Copy with dates in the future it will do a better job than year-end-copy. The YEC has to try to work around reconciled vs unreconciled transactions and the Copy doesn't.
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