1.Create a new calc spreadsheet, enter something in any cell.  Save the spreadsheet but leave the window open.
2.Create a second new calc spreadsheet.
3.Turn change tracking on (edit > track changes > record changes.)
4. Click on a cell, enter =, then click on the cell you filled in in step 1, hit return.
5. The cell you filled in in step 4 should now show the value entered in step 1 (and if you look at the formula that has been entered it will start "='file///…")
6. Delete the contents of the cell.
7. Save and close the second spreadsheet.
8. Open the second spreadsheet.
You will get a message (which message you get depends on the version of LibreOffice) saying your spreadsheet has links to an external file and giving you the option of following them.

As best I can tell, the only way to stop the message (other than enabling automatic linking) is to stop recording changes, which of course loses ALL change history.
(I've tried accepting or rejecting the change on just the cell in question and that doesn't stop the message.)

I believe the problem is that because the change history remembers the external file link even after the formula containing it has been deleted (or replaced by something else) the program attempts to follow it when the spreadsheet is loaded, even though the result won't actually be used.  This is even true if the change deleting the external has been accepted: the change history still remembers the old value as having been changed.

I believe the "right" implementation here would be to process external file links only if the result will be "used" in the spreadsheet.  (I don't know what happens, or, to be honest, what should happen, if an external link is in a conditional expression of some kind and is used dependent on what the condition evaluates to, although that may be a related issue.) 

This "bug" (behavior) is present in 3.3, 6.0, and 6.1.0.0beta1.