The simple answer is no.
If you make air move, in the audio range of humans, and not too quiet, then there is no duration short enough that it can't be heard.
And a millisecond is a very long period of time for the human ear to react to a sound.
Your options are:
use ultrasound, as you mentioned
use very low volume (may or may not work for you)
Ask for a gameplay video showing different scenarios in game and start working on sounds on top of that video. I've found it's much easier in most cases than trying to describe things just with words. Later you can use this video to show the client how you would have implemented the sounds in game.
If possible getting an unfinished version of the game could ...
Ask them for a few (like 3) references for games they are playing that are roughly similar to the game they are making. Go play those games and make video captures. Copy some of the key sounds you think would work from the reference games. Use these copies as a starting point for your new original work.
Keep in mind that everyone needs to hear the sounds in ...
How about embedding a smart contract into the audio using digital watermarking?
Essentially, a trusted encrypted ledger entry could embed the date (or any particular information) such that later on you could retrieve the value and compare it against what is in the ledger.
Don't know if that's a thing, but it sounds like it could work.
This might be a forensics question, the answer to which is is the ENF signal (Electrical Network Frequency) which is used in forensics to locate certain associated acoustic and electrical signals in time for forensic purposes
ENF is a technique commonly used in audio forensics. It requires analysts to have recorded ENF signals over a long period of time.
You're not gonna like this. The only for-sure way of lining up audio files is to have them All the same length to begin with, including the silences. So when you record them, make sure you start from zero with each file, even if it only has one bleep five minutes in! Lining up varying length soundfles is a nightmare otherwise.
I don't think anyone would advise you to migrate your tracks/stems using the mp3 format.. especially when using them with uncompressed files in the same project. Not forgeting the loss of quality/imagery in your production.
Recommend mp3 only as a final mix format for distrobution on iTunes etc..
The best advice I can give is to ask questions. As a sound designer, you are the subject matter expert when it comes to designing a sound, not the client. The client may very well not know what they want. Ask about what the purpose of the sound is. Provide feedback and ideas on how that need can be met. Listen to their responses and flush out what it is ...