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.