The process used to bring Holmes Back from the Dead permanently dyed his hair from black to blondYes, this requires ignoring the Victorian flashbacks when Holmes' hair was blond as well. But his hair does appear to be at least a dark shade of brunet when he's shown in suspended animation.
Holmes is in denial about Robo-Watson's status as a Replacement GoldfishOverall, he tends to treat Robo-Watson as the geniune article. But there are little moments when he catches himself, such as when he refers to the Victorian ages as 'their time' before correcting himself. Considering that Canon!Holmes once called Watson his only fixed point in an ever changing age, it's not that surprising that he'd cling to the closest thing he has in an unfamiliar environment.
Holmes is heavily depressed and, furthermore, attempted suicide shortly before the events of The Red-Headed League.He has overtly stated that defeating Moriarty is his only reason for existence. His home, noted for its typical state of clutter, is frankly much neater than an IKEA demonstration room. He no longer plays his violin, having given it up for a simpler, keytar-like instrument. He has not been seen to do chemical experiments or engage in his usual eccentricities. The only things we ever see him do are work cases or sit around quietly at home. He's usually outwardly quite cheerful, compared to how he behaves in Watson's journals. And then, in The Red-Headed League, he seems unusually pale, as if from some time spent indoors recuperating, and he suggests that he and Watson go to an art gallery—partly for the case, but he seems to be genuinely interested in the art. Looking for a distraction? Trying to use a social outing to apologize for scaring his friend? This editor is convinced of it.
The Bravestarr episode is in canon with this series.Holmes actually did go through the time warp that brought him to Bravestarr's 23rd century, and he had adventures there, but he finally found a way to return home to the 19th century, where he lived out the rest of his life. However, because he now knew the technology would one day exist to revive him (after all, it had worked for Moriarty), he made the bizarre-seeming arrangements to have his body preserved in honey. Sure enough, he got revived in the 22nd century. This explains why has so little emotional difficulty fitting in to the new world. Using his future knowledge to arrange an early revival may have produced a divergent timeline, since the 23rd century characters appeared to have no knowledge of his having been around in the 22nd. Officer Beth Lestrade is probably related to Inspector Kitty Lestrade from the 23rd century, and (if the timelines do not diverge) may even be her ancestor. Presumably, Holmes's electrical powers faded at some point.