How many times is OK to register for a PhD program?
The fundamental issue here is that your first advisor left academia altogether—by retiring before his students were done. This is an awful thing to do to the people one is supervising—leaving them completely in the lurch in such a manner is unacceptable behavior. The advisor should not have taken on new students if he was planning on retiring. 

As a result of this, it is obvious that some allowances for this will need to be made. The way to signal this is through your CV: list both advisors, including the dates for which you worked with them. If your first advisor is well-known enough, then this will automatically clue in others about what happened. 

Overall, though, so long as the time required isn't too unreasonable for your discipline, an extended stay in graduate school isn't problematic. However, if you have mitigating circumstances such as these, it makes such problems a lot easier to overlook.