Ok so I was making my way to Virgil and when I finally reached him and persuade him to spill out all he knew I got a message:

''Failed: Talk to the settlers at Abernathy Farm''.

I had to load like 9 saves into the past to be able to head to the farm in time and not fail that mission. All those saves and progress lost, all those cool weapons and armor found in the Glowing Sea from legendaries gone...

So how do you actually know witch missions have a timer and how can you find that timer, if it exists ?

As far as I can work out, only the Minutemen and settlement defense missions have a timer. There may be others, but so far those are the only ones I left long enough to auto complete/fail.

Another to add to the list of auto-expiring missions... "Investigate Vault 81".

I spotted the vault 81 dude, cleared his escort and he took off like a rabbit. I forgot about the objective for what must have been a couple of in-game weeks and suddenly got a "Completed : Investigate Vault 81" message. I was nowhere near the place.

From a RP point of view, I was not too bothered as I had never received any clue as to where it was or why I should go there other than "Hey, there must be another vault somewhere. I wonder if there are folks still alive or if he just stole a vault suit?".

Mm, didn't know of that Vault one. To my knowledge, only timed quests are

a) Defend quests, which you get automatically at times though getting them is extremely easy to miss. I believe there are couple mods that either stop them from happening, or show actual message window when you get them instead of just flashing the text in upper left corner.

b) Kidnapping quests. These can be avoided to a point by not accepting them, or not hearing about them (avoid Preston ) but once you have got them in your quest log, you need to complete them in fairly timely manner.