Answer heavily drawn from the Wookiepedia article for the Lost Twenty in Legends.
Given the apparent discrepancy of numbers, the idea that the Lost Twenty only represent Jedi Masters who left the Jedi Order during the thousand-year peace after the Ruusan Reformation may seem to make sense - a new, modern chapter in the history of the Jedi, during the Golden Age of the Old Republic. A time when the Sith is apparently no more, so the departure of any Jedi Master would be an even bigger deal than in the dark times before. However, that is clearly not the case:
One of the earliest members of the Lost Twenty was the Umbaran Jedi Master Phanius, who eventually became Darth Ruin, the first Dark Lord of the Sith in the New Sith Empire. Over time more would leave; twelve by 990 BBY, and ending with the twentieth member, Master Dooku.
A quick history of the Sith as a backdrop:
- 7000 BBY: The first group of fallen Jedi to call themselves Dark Jedi is formed. Defeated, they were exiled and later discovered the Sith race.
- 6900-5000 BBY: Sith Empire
- 4980-before 2000 BBY: Sith Empire (Restored) - SWTOR is set during this period
- 2000-1100 BBY: New Sith Empire (Founded by the earliest named Jedi Master counted among the Lost Twenty)
- 1010-1000 BBY: Brotherhood of Darkness
- 1000 BBY: Commencement of the Rule of Two by Darth Bane
What we can tell from here is 1) Jedi Masters are already being "Lost" since before the Ruusan Reformation 2) Darth Ruin does not appear to be the first.
We don't know exactly when the first Lost Master left - he may or may not be a major character in the EU. It is possible that the Lost Twenty is indeed a list of all Jedi Masters who have ever left the Jedi Order in all of their recorded history, but we cannot say so conclusively.
Nonetheless, why are there only Twenty when we know so many Jedi left the order? The answer is because the Lost Twenty only count Jedi Masters. That much is obvious. A more complex question would be: Are there really just Twenty Jedi Masters who left the Jedi Order? If not, why are only these Twenty honoured by the Order? There is no direct answer available from Legends sources, but the following excerpt offers a hint:
Along with the most venerable Masters, the Lost were remembered in the form of busts in the Jedi Archives; a reminder of the Jedi's greatest failures, though the Jedi did not fault the individuals for leaving, regarding the statues as a reminder that the Jedi were not perfect and that sometimes they might fail to provide what a Jedi might seek out of life. On each bust's pedestal, the great deeds of the Master it commemorated were listed, though it gave no mention of why he or she left the Order.
Jocasta Nu also had this to say during the movie:
"The Lost Twenty. And Count Dooku was the most recent and the most painful. No one likes to talk about it. His leaving was a great loss to the Order."
This suggests that, for you to be counted among the Lost, the following general conditions should be met (not verified as 100% correct):
- You are a Jedi Master
- You are leaving on your own accord
- The Jedi really doesn't want you to leave
- Your departure is considered a great tragedy to the Order
It is possible that there really are just Twenty Jedi Masters who have ever left since the Jedi started keeping track. We cannot conclude decisively. But if there are Jedi Masters who voluntarily leave the Order but aren't added to the Lost, it's probably because the Jedi don't love you enough.
Why, then, did Obi-Wan say
"Only twenty Jedi have ever left the Order."
as opposed to "twenty Jedi Masters"? Well...maybe to him the existence of anyone lesser than the rank of Master does not even register in his eyes after they are dead and gone?