Consider the following text: "It is a bicycle. How do we know it is a bicycle, though?". Would this be a reasonable use of though in formal writing (in an essay)?
What are the ways of avoiding this construction if one would want alternatives (except for skipping the though)? Would however, for example, work? The question doesn't really contradict what is stated, though.
"However" functions as a more formal version of adverbial "though", this mainly due to an informal appeal to the reader that "though" suggests when it comes at the end of a sentence. On a different note, it doesn't always imply a direct contradiction. It could simply imply a qualification or contrast to what has already been stated.
For example, you could use it to qualify something to avoid confusion.
"I'm sick. I still would like to meet for coffee, though".
On the contrary, you could use it to contradict a previous statement.
"My boss told me not to come to work because I was sick. I had too much work to do to stay home, though".
In your example,
"How do we know it is a bicycle, though?"
might not (we'd need more context) contradict whether it is a bicycle or imply any contrast, but rather seek to qualify its bicycle-ness.
If you were compelled to change the wording, here are three options that incrementally emphasize the qualification:
"It is a bicycle, but how do we know it is a bicycle?"
"It is a bicycle, yet how do we know it is a bicycle?"
"It is a bicycle; however, how do we know that it is a bicycle?"
