I heard some talk in chat that swapping skills incurred the 5% time increase penalty, though I haven't heard anything confirmatory from TS about it. We do know that if you use favor to speed up a skill, and then swap to another skill, when you swap back to finish the skill you will not be able to favor-boost it again.
For the purposes of the number of skills you can know when calculating training times, a skill is considered "known" as soon as you begin training it. If you're past the threshold where training times are increasing, this will retroactively increase the training times of all your paused skills as well. So in this regard, there is indeed a penalty for pausing a skill if you are doing so to begin training a brand new skill. I am not aware of any other penalty for it though; you don't technically lose any progress you've made toward the skill, but if you start up a bunch of other skills before returning to it you may find that its remaining training time is back where it was when you originally started it or even potentially higher.
I confirmed all of this myself yesterday.
EDIT: I did not know about that favor thing... wish I'd known it this morning! ; ;
I didn't eveen notice you could swap skills! thanks for the heads-up! but since i'm a day into my 4 day BL5 and i've donated loads to speed itt up, i can't swap right now. too bad, i want to be a mastertink pronto! x
Also worth noting that if you haven't learned all the Better Learning levels, learning a new BL level will reduce the time cost of the paused skill accordingly. (I.e., the time to learn of a paused skill is not frozen in either direction.)
I thought that if you paused the skill the time was locked in, but that it still counted as being completed, thus raising the number of skills you know and increasing the time required to learn new skills? I didn't know the paused skills would have their times retroactively increased.
They are now retroactively increasing the skills. At one point, it locked them in, so I paused TP5 at 3.5 days and decided to learn other things. Bad idea...
If you switch skills, you lose any sped-up learning that you are currently experiencing. If you switch and switch back, you can still speed up the original skill through favor-boosting. I'm currently doing that with Better Learning V. At least last time I checked this was so. Things keep changing...
I just checked myself, and it is false that you lose the ability to favor-boost the skill. I'm able to favor-boost a previously favor-boosted skill that I swapped out to finish another skill. Just wait for the speed bonus to run its course before you swap and you'll be fine (it will give you a warning if there's a speed bonus in effect).
If you start a skill it counts towards the total of skills learned to add time on - thus when the skills start taking longer after 20 they count towards the 20.