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I've faced this as well. One of the big sources of "mess" for me in a years-long ledger is inconsistencies in account naming. I get around this with a big block of alias that rename accounts to use my newer, preferred conventions (without having to comb through possibly hundreds of postings to update by hand).

I also went through a couple file organization schemes and have (tentatively) settled on file-per-month since that leads to a nice cadence where setting up the new monthly file coincides with paying bills and is a good time to do any necessary account reconciliation.

PTA does give you a lot of flexibility, sometimes too much. More guidance/opinion on this is probably needed. https://plaintextaccounting.org/Organising-files talks about it a little. Also if you make it to any of the support fora/chat rooms, you'll usually get help on this.

I just put everything in one file. Over 15 years worth of transactions in a single ledger file ordered by date.