Student or Learner
Can we always replace how long with since when?
How long have you been here?
Since when have you been here?
Not always. In the example you gave, either one works. If the clause that follows is in the present perfect ("have done") or present perfect progressive ("have been doing,") I think you could probably use either. If the clause is in the past, however, and the action is no longer continuing, "since when" would be incorrect.
"How long did you play minor league baseball?" (I'm aware you no longer play.)
"How long was Anne Frank's family hiding from the Nazis?" (I'm aware they're no longer hiding.)
"How long had he been working undercover before his true identity was discovered?" (In this case, it's obvious to anyone listening that he is no longer working undercover.)
You could not use "since when" in any of these cases.
"Since when" is also used informally with the present tense to indicate surprise or suspicion.
"Since when do you wear a suit to dinner at your mother's house?" (I'm surprised to see you wearing a suit to dinner at your mother's house, because I've never known you to do that before. I might even be suspicious and think you're lying about going to Mom's.)
"Since when do you care about the environment?" (Perhaps said in response to someone explaining their actions as "for the environment," when he had never previously expressed such concern.)
"Since when are you a vegetarian?" (You ate burgers just last week; what's going on?)
"How long" does not convey surprise or suspicion, and is not used with the simple present tense.