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.
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