Here is a post from the MoneyWorks forum on things you should be doing in MoneyWorks at the end of the financial year. If you are using stock/inventory, the one thing you should remember to do at the end of business on the last day of the year is to start the MoneyWorks Stocktake, which takes a snapshot of your current stock holding and values.
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Backup the Company file and post all the stock related entries, then go to the Command menu > Stocktake > Start Stocktake to start your stock taking process.