"This Workbook contains links to one or more external sources that could be unsafe."

I know this is a few years old now, but I just had the same pop-up box everytime I opened one of my Profits & Losses Reports. After meticulously checking, double checking, and even breaking and reentering the formulas for the data, then I found the solution for my particular problem. The Workbook Links had been set to 'Ask to refresh'. 

To fix this,

Click on File, then Info, then the 'Edit Links to Files', from there click on the settings gear, select 'Always Refresh'.  

Problem solved with the annoying pop-up box saying "This Workbook contains links to one or more external sources that could be unsafe. If you trust the links, update them to get the latest data. Otherwise, you can keep working with the data you have."

There was no problem with my data or the links, I'm guessing in an update MS changed that setting to 'Ask to Refresh' 

Good day!