I assume by 'linked files' you mean these:
calibre-complete.exe, calibre-customize.exe, calibre-debug.exe, calibre-parallel.exe, calibre-server.exe, calibre-smtp.exe, calibredb.exe, ebook-convert.exe, ebook-device.exe, ebook-edit.exe, ebook-meta.exe, ebook-polish.exe, ebook-viewer.exe, fetch-ebook-metadata.exe, lrf2lrs.exe, lrfviewer.exe, lrs2lrf.exe, markdown-calibre.exe, web2disk.exe.
I've occasionally had the same 'problem' with other application installs. But I see it more often with Calibre because it's updated more often than other applications. And I'm pretty sure it only ever happens with MSI installs - but not every time, and not all MSI installs. I've had the same message from a SQLite Browser install, it only has two executables - it also uses Qt.
To avoid this sort of issue I always do application software installs after a cold boot (a practice I adopted on NT4 and OS/2). And, I don't run calibre.exe or any of the 'linked files' from startup. And, I've checked the Create Date timestamps on those files when the message pops, and they're all within the last minute or two.
On one occasion I took a copy of Program Files/Calibre2, did the restart, and then did a compare using Beyond Compare - nothing changed.
I can't imagine how it could be, but I'm half inclined to point the finger at Qt
But I would put my money on a quirk in the Trusted Installer.
BR