If you delete a map while it is marked to be cooked in a custom profile, then run the custom profile the map won't be deleted from the profile .ulps.
I wasn't able to launch using the new custom profile. It threw an error when it couldn't find TestMap2.
Workarounds:
Add maps to content with exactly same names, then open Project Launcher's custom profile, unselect these maps and then delete maps from content.
Navigate to <Engine Version>/Engine/Programs/UnrealFrontend/Profiles directory, open profile configuration in text editor and manually delete map entries.
Found in 4.24.2 CL#10758860
Reproduced in 4.23.1 CL#, 4.25 Main CL#11302131
1. Create a blank project. Create 3 maps named TestMap1, TestMap2, and TestMap3. Make sure to have TestMap3 open.
2. Open the Project Launcher and create a new custom profile that has all three maps marked for cooking.
3. Return to the content browser and delete TestMap2.
4. Run the custom profile.
Result: A warning will appear about TestMap2 not being found and cook fails.
Expected: The cook works without any issues.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-88438 in the post.