I have a python addin that might help you find the broken links without having to actually open the mxd. in case the above doesn't work and you need another option Python addin for data inventory and “broken-link” repair.
Thanks! I will definitely give that a try. Unfortunately, Esri support hasn't been very helpful with this.
I got a pretty easy work-around from esri. I copy the MXDs to my desktop, disconnect from my network and the internet (Network and Sharing Center in Windows 7), open the file (it took less than 30 sec), then re-connect to the internet and my network, fix all the broken links and save it to its original location. It was MUCH faster than waiting for the mxd to open or trying to fix the broken links in Catalog.
Alternatively to that you can right click on the MXD in ArcCatalog and select Set Data Source

But you may still have issues with it being a 9.3 MXD
Yes, that is the easiest and most obvious solution, which I had already tried.
It didn't matter if it was a 9.3 or a 10.2 document, it would take forever to open in ArcMap, or to bring up the data sources when right-clicking in Catalog. The issue was with the data sources; SDE had been moved and renamed when we upgraded to 10.2. The MXDs had previously opened easily in 9.3 but would open very slowly (or not at all) in 10.2. I experimented with saving the MXDs in 10.2 and NOT repairing the data sources - the issue remained. This was the work-around esri gave me for the problem.
Thanks! Unfortunately that didn't work for my problem. On or Off, ArcMap is still looking for the missing data sources. The solutionMindaugas Rasiukevicius had (and the one I was given by esri) seems to work the best.
That's a handy tool, though. I definitely can use it with other documents!
Try attached tool,
Store MXD with issue in a folder.
Run the tool,
Select above folder,
select any .sde connection file which is working
This will replace every SDE type data in mxd with new .sde location you provided. Thus replaces all your current layer connections 'including raster' to this. Try opening the map document, resource the layers then.
Thanks
Abdullah Saleh