Posit: Sherlock is only wearing the sheet to Skype. He usually wears nothing around the house.

Sherlock walks around the house wearing only a sheet, potentially maybe even less.

Sherlock often doesn’t seem to notice whether John is actually around or not.

If you were prone to bouts of partial or full nudity that you didn’t want anyone to witness, you’d pay more attention to the location of your “flatmate” to prevent embarrassing mishaps.

I infer from this that Sherlock walks around in this state whether John is in the room or not.

If you’re going to be so obvious, then why not say that Sherlock walks around naked all the time? Pff. 

I’ll go a little further with the observations, if I may:

Observation #1: At the point we enter the conversation, Sherlock already has his laptop open in the kitchen and has made himself a cup of tea or coffee. Inference: he was already talking to John via Skype before temporarily going back into the bedroom.

Observation #2: When he comes out of the bedroom he has nothing in his hands - nothing that he might have been going back to retrieve. Also, John feels embarrassed. He must have gone back into the bedroom to cover himself up with a sheet, then, probably at John’s request.

Observation #3: It doesn’t seem too early in the day and yet Sherlock seems sleepy. Obviously he was up rather late, then. (That drink is probably coffee not tea).

Observation #4: John was in Dublin the previous day. Since he’s somewhere rural now and it’s probably still morning (unless Sherlock was up really late) it seems unlikely he’s been back to London yet.

Conclusion: Sherlock had the laptop in the bedroom with him (no doubt because he was talking to John in Dublin late into the night after going to bed). His sleep was interrupted by news about a new case - on learning where the crime scene was he contacted John to send him to the location. He then went back to sleep, then once John was at the scene he woke Sherlock up again via Skype. Sherlock, needing coffee, got up without bothering to dress, carried Skype-John into the kitchen, talked to him while strutting about naked making coffee before finally giving in to John’s pleas that he go and cover himself up. Because late at night is one thing, but mid-morning on a crime scene with a bunch of police officers looking over your shoulder at your naked flatmate is another.