Some start menu shortcuts are missing on Windows 10

I had a similar problem after upgrading.
I was able to fix it by:

• Going to Start Menu folder->Properties (%appdata%\Microsoft\Windows\Start Menu)
• Selecting the "Hidden" option
• Hit "Apply"
• Select "Apply changes to this folder, subfolders and files" and hit OK
• Unselect the "Hidden" option
• Hit "Apply"
• Select "Apply changes to this folder, subfolders and files" and hit OK

I'm not sure what caused Windows to see some as hidden and others not, but this reset the flags and everything is visible on the start menu, now.

I found out a peculiar behaviour which causes an instance of this problem.
My findings are for build 1703, and I cannot, at the moment, verify them on more recent builds.

I had a shortcut inside a menu folder which would not show up, no matter what.
In the end, I discovered that the Start Menu hides duplicate shortcuts that point to the same file. Suppose you have a shortcut named Shortcut-A at the root level of the menu file structure (C:\ProgramData\Microsoft\Windows\Start Menu\Programs) which points to c:\someprogram.exe.
Now suppose you have a copy of Shortcut-A in a menu folder e.g. C:\ProgramData\Microsoft\Windows\Start Menu\Programs\SomeFolder.
In the All applications list only the copy at root level will be visible. You can find the folder SomeFolder under the letter "S" in the list, but the shortcut will not be visible under it.
Furthermore, this happens even if the two shortcuts have different names, but point to the same executable. In other words, if, in SomeFolder, you have Shortcut-B pointing to c:\someprogram.exe it will not show up as well.

In my tests this can be reproduced systematically and the Start Menu immediately updates itself after creating/deleting copies of the shortcut, with no need to touch the menu database files.

At the current moment the start menu is limited to 500 entries in the database. This also affects search and Cortana as they both rely on that DB.

There is currently no known fix other than going to your start menu folder and deleting links and folders to apps not used.

Edit: On 2015-09-19 they released a technical preview that lifted that limit to 2048, which is nice. It should be pushing out to Insiders and will trickle down to standard users soon enough.

Source: http://arstechnica.com/gadgets/2015/07/review-windows-10-is-the-best-version-yet-once-the-bugs-get-fixed/