I want to know the meaning of 'it seems' from the perspective of 'certainty'.
If someone says that:
It seems that the file has been deleted.
Could it be possible that he is making this claim based on something other than checking the actual file, which could still be present, that something wrongly implies that the file is absent.
I would like to know that how confident people are about the validity of something they use 'it seems' to declare.
In the context you inquire about, I would say that "it seems" suggests a high degree of certainty, but leaves a bit more wiggle room than, say:
I guarantee the file has been deleted.
and it's a little "softer" than:
I know the file was deleted.
If I was less certain about the deletion of the file, but I still thought it was a distinct possibility, I might opt to say:
The file might (or may, or could) have been deleted.
Where I'm even less confident, but it's still something that ought to be considered:
It's possible that the file was deleted.
I don't know if one short answer can cover all the possible contexts where it seems could be inserted, so this shouldn't be considered an end-all answer. For example, sometimes we use "it seems" (or "it may seem") when we are sure something isn't true (but we want to express how it appeared likely, at least at first):
It seemed like Linda had murdered her husband, but then the police found a clue that exonerated her.
The water seems cold when you first get in, but after you start swimming, it's not so bad.
The scale of epistemic modality from strong positive to strong negative would look something like this:
The file has definitely been deleted.
The file has been deleted.
The file has probably been deleted.
I think the file has been deleted.
It seems that the file has been deleted.
The file seems to have been deleted.
The file may have been deleted.>
The file may not have been deleted.
The file seems not to have been deleted.
It seems that the file has not been deleted.
I don’t think the file has been deleted.
The file has probably not been deleted.
The file has not been deleted.
The file has definitely not been deleted.
From this you will see that seem suggests fairly strong probability, in both positive and negative directions.
I think the giveaway here is OP's based on something other than checking the actual file, suggesting he interprets it in it seems as referring to the actual file. But in fact, the it here is the dummy/existential "it".
By implication there must be an observer to perceive everything relevant to the overall situation, and to conclude that the file appears to have been deleted. But native speakers don't normally interpret OP's construction that way. That's to say, "It seems that X" doesn't automatically mean mean "It seems to me that X [is true]". We tend to interpret it as "Anyone who considers the overall situation would gain the impression that X is true", or simply "It is likely that X is true".
Thus, it seems doesn't necessarily have any implications for whose observations and judgements lead to the conclusion [that the file has been deleted]. In OP's case, the speaker could be a senior manager reporting the fact that his entire staff have been searching for the file all week, and it seems to them that it must have been deleted, since otherwise they would have found it by now.
I hope that covers the issue of seems to who, so I'll turn to the matter of how certain something is when you use the it seems construction. The first point to note is that if it seems to be true, this always implies it's more likely to be true than not true. But it could imply anything from "likely" to "absolutely certain".
It's quite possible someone has just said to our speaker "You know that file you were asking about? Sorry, but I deleted it yesterday, including all backup copies!". Our speaker might quite naturally relay this information to someone else as "I'm afraid it seems that file has been deleted."
I included I'm afraid in my rephrasing there to show another similar usage - which performs much the same role as it seems, and thus emphasises it. The speaker certainly isn't literally "afraid" of anything, nor is he expressing any doubts as to whether the file has in fact been deleted or not. It's an absolute certainty, and he will expect his audience to understand that. He could have simply said "The file has been deleted", but he precedes it with a couple of hedges to soften the impact of the "bad news".
Finally, I'll just offer this from New Scientist:
However, it seems that it has not been possible to make the Brookhaven machine produce the intensity of fast protons originally expected of it.
...where there's absolutely no question that it has not been possible to achieve the expected results, and it's irrelevant to speculate on who might be making a "judgement based on appearance".
In short, it seems isn't really about who it seems to, or how likely it is. It's a "hedge" which is usually used to mitigate the effect on the audience of stating something that may be either probable or certain.
In this case the phrase it seems is a contraction of it seems to me, meaning the way I see it, or my hypothosis is that.
Consequently we can see that the phrase is the same as
I have concluded that the file has been deleted
Generally speaking this phrase is deployed to note that the conclusion has been reached by eliminating other possibilities, rather than due to evidence of the conclusion itself. There's often an emphasis on there being no other avenues of inquiry left to the speaker, and that the only option left is the one that "it seems to me must have occurred".
For example:
I've looked in the Recycle Bin, your My Documents folder and on the Desktop, and I can't find the file anywhere. So it seems that the file must have been deleted.
In this sentence, the author has tried a variety of options and investigated a number of paths, and has finally ran out of options, leaving only the possibility that the file must have been deleted.
