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If you're using CheckBook Pro, after the import, you may just have to select each individual Entry all together by holding down the Command key and going through and clicking each Entry. After that, hit the Change button, check off the field you'd like to change, and type in the new information.
Otherwise, you might try duplicating the QIF, opening it up in TextEdit, and using the 'Find and Replace...' option under the Edit menu to switch out the items. With something like the Payees field, the listings are preceded by a letter P, so by finding a particular item like "P[MY BANK CHECKING]", you can choose to replace that with "PMY BANK CHECKING" to quickly remove the brackets for what'll end up in CheckBook's To/From field.
With the idea of switching 'To/From' to 'To Account/From Account', unfortunately there's probably no workaround. However, the imported transfers should come in with the two corresponding Entries in both Accounts. Meaning, your transfers will be treated as they should with one item acting as a deduction from the origin Account while the other corresponding item gets added to the receiving Account—those items just won't be truly linked like Linked Entry Transfer created in the application.
_________________ Allan WoodallPhosphorescent PhageSplasm Software http://www.splasm.com
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