I have found that when you enter a hyperlink into Excel Online, open in the Excel Rich Client, Save, and then re-open in Excel Online, the hyperlinks are updated and subsequently broken.
So if you enter a hyperlink (in Excel Online): https://contoso.sharepoint.com/Documents/2017 Financials.xlsx?d=<guid> it will be changed to a relative link: 2017 Financials.xlsx?d=<guid> and you will see the below error when you click on it in Excel Online.
This is because, in the Excel Rich Client all hyperlinks to files are automatically updated before you save to ensure that all the links are up-to-date at the point of save.
There are two ways to fix this.
1). Use the =HYPERLINK() function. If you use this function, the hyperlinks will not break.
2). Disable the updating of these links in the Excel Rich Client, by going to Excel Options > Advanced > General > Web Options > File names and locations > and uncheck Update links on save. If you disable this, the hyperlinks will not be updated in the Excel Rich client and therefore will not be broken in Excel Online.
Here is the Registry Key to disable "Update links on save", in the event you need to push this out to more than one person.
I have brought this up to our product group.