Based on my research, Migration tool won’t change or replace previous link URL in Excel workbooks even if the linked files are uploaded to Sharepoint Online, we need to re-add the links again. If there are many linked files, this does require a lot of manual effort to create these links.
So far, about the auto fix tool, I find a similar thread "Tool to auto fix broken excel links after migration to SharePoint online", hope it could help you.
Thanks for your understanding.
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