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Full Disclosure: I am playing the game using Wine in Linux, so this might be Wine-specific.

I came across a bug in the game, where the countdown timer (which is used in the first stealth mission) is missing from the screen when the "scaled" option is set to "1.4x". I suspect what is happening is that the timer's placement is not being adjusted with the scale, and is positioned below the bottom of the screen.

If you are playing a level where the timer is supposed to show up, but isn't, try changing the scaling to "1.0" for that level, and you should have the timer visible again.
this is not Wine-specific, I ran into the same problem in the Sneaking mission while playing on Windows 10 with resolution set to 1920x1080 and scaling to 1.4.

I didn't even know there was supposed to be a timer until I started to fail the mission by randomly de-cloaking with no apparent reason.