Actually really think about it. Lowrie had wrist problems that held him out in 2009. In 2010, his wrist was completely healed, and the only reason that he missed any playing time at all in 2010 was because of mono.
Now if you want to call Lowrie injury prone because he got mono, then we need to stop here because that's just where we disagree. Anyone can get mono. I got mono 5 years ago, and I can promise you that after a year of recovery, it has no ill effects.
Youkilis missed 1/2 of the season last year with a torn tendon in his right hand. It was an injury that is extremely rare in the sports industry, so if you ask me, the recovery from that seems much more questionable than the recovery from a 2 year old wrist injury + mono.
Not picking sides here, but I think it's pretty valid to have just as much concern about Youk as it is about Lowrie for the upcoming season, purely based on how recent and serious each players injuries were.
Having said that - I don't think Youk will have any problems at all transitioning back over to 3rd base. Like you said, he's a 3rd baseman turned to a 1st baseman, not the opposite. He's going back to his natural position, so I have no worries about that.