The way I understood it is that in this particular case we have two separate timelines to keep track of: the Hunter C-20's, and Sylvie's.But Sylvie is at that point existing in the same timeline as the hunter - so from her perspective its still hundred of years ago, which implies their shared timeline is in the future. Also Sylvie having spent years on the plan would suggest that there is a shareable time reference.
Based on last weeks dialogue about Duplicate castings being identical at the molecular level, I wonder if Sylvie is in reality the mindwiped molecular duplicate of Loki-A from a future in which Loki died - She's Sylvie Lokisdotter
The Hunter's timeline goes like this:
1. Lives a life on what seems like modern-day Earth.
2. Gets involved in something timey-wimey and is labeled a Variant.
3. TVA "recruits" her.
4. TVA does something to her memory and then she spends a few hundred years doing TVA stuff.
5. When investigating the RenFaire incident in the 1980s, she gets kidnapped by Sylvie and taken to the Roxxcart mall in the 2050s.
6. Sylvie puts the mental whammy on her.
Sylvie's timeline instead goes like this:
1. Various undisclosed stuff.
2. Attacks TVA agents investigating a thing in the 80s, and kidnaps one of them.
3. Takes the kidnapped TVA agent to the 2050s.
4. Puts the mental whammy on the TVA agent in order to learn stuff about the time keepers.
5. The stuff we just saw in episode 3.
So C-20's 5-6 co-incide with Sylvie's 2-4, but the "hundreds of years" Sylvie refers to are C-20's step 4.
On a related note, I wonder if TVA agents actually become unaging or if the TVA works the same as Death's Domain in Discworld: time doesn't pass there so you don't age while inside, but if you go back to the "real" world you still age in normal time.