Hi @Darwin Goh ,
There is no available migration tool to migrate linked excel files without breaking links. You could use SharePoint Migration Tool to migrate files from file share to SharePoint online then use some other third-party tools to fix broken excel links.
For Reference:
Tool to auto fix broken excel links after migration to SharePoint online
Migrate Excel files with a lot of links to SharePoint Online?
If the answer is helpful, please click "Accept Answer" and kindly upvote it. If you have extra questions about this answer, please click "Comment".
Note: Please follow the steps in our documentation to enable e-mail notifications if you want to receive the related email notification for this thread.