Pro version 3.1.3
I've been running into this problem recently.
In short, using the Exclamation point to fix broken links has limited functionality.
TLDR: the Exclamation point will repair Esri data types (except mobile geodatabases) + and maybe one thing else, even if everything is in the same folder.
This is not a problem if using the catalog pane to update a map's sources with a find/replace.
In the screenshot below, I have several layers and views pointing to data of the following types:
- TINs
- File Geodatabase Vector and Tabular Data
- Mobile Geodatabase Vector Data
- CAD data
- Excel Data
- Shapefiles
- KMLs

Here's the thing. All of these data sources, as you can see, are in the same folder.
If I use the exclamation point to repair the sources, I get the following results:
Note: I am starting from a fresh map each time.
Thing repaired | Yield | Picture for proof |
DBF or SHP or TIN or file Geodatabase Contents or standalone rasters | - SHP,
- TIN,
- DBF,
- Standalone raster datasets
- File Geodatabase feature classes and tables
- Also caused graphical bug where the broken file geodatabase persisted despite having nothing pointing to it.
|  |
CAD data | - SHP,
- TIN,
- DBF,
- Standalone raster datasets
- File Geodatabase feature classes and tables
- And exactly one repaired CAD layer, even though there are 10 others in the same place
|  |
Mobile geodatabase | - SHP,
- TIN,
- DBF,
- Standalone raster datasets
- File Geodatabase feature classes and tables
- Mobile Geodatabase contents
- Also caused graphical bug where the broken file geodatabase persisted despite having nothing pointing to it.
|  |
Geopackage | - SHP,
- TIN,
- DBF,
- Standalone raster datasets
- File Geodatabase feature classes and tables
- Geopackage contents
- Also mistakenly repaired the link for layer pointing to a feature class of the same name in a mobile geodatabase
|  |
KML | - Repaired that KML and nothing else
|  |
Excel Sheet | - SHP,
- TIN,
- DBF,
- Standalone raster datasets
- File Geodatabase feature classes and tables
- That Excel sheet
|  |
Please improve the functionality of this workflow to properly repair all data sources at once.