An odd double word sentence, is it acceptable?

Is it grammatical? Yes. This is a matter of style. Your sentence sounds a bit odd, however, but not for the reason you suggest. More about that later.

Note that it's not even bad style to repeat a word immediately if the sentence makes sense and is clear.

"Honesty? He discovered that that was the best policy after all."

Nevertheless, style is a matter of personal preference. If the doubling in your own sentence bothers you, recast the sentence. For example,

"I detailed in my journal the projects I had a hand in."

There's always a different way to say something. Find one that suits you.

Now, about the sentence as you gave it:

"I detailed the projects I had a hand in in my journal."

That is a bit ambiguous, since the sentence could refer to detailing in your journal those projects, or detailing only those projects that appear in your journal. My suggestion above assumes the former, but if you mean the latter, recast to make that clearer.