If you stand within range of a beacon with a Level 2 effect, then drink the same potion type with a Level 1 effect, then leave the region, your longer lasting Level 1 effect gets removed along with the Level 2 effect.
This also happens if you drink a potion of speed 2 and then drink a longer lasting potion of speed 1.
This happens because the lower level effect is not tracked - only the highest new level effect is stored. The HiddenEffect nbt tag only updates when the new effect is higher than the current effect, thus fails when the opposite happens.

To reproduce:

1. Create a beacon with level 2 speed. Alternatively, drink a potion of level 2 speed. Alternatively, run:

/effect give @s speed 5 1 true

2. Drink a Level 1 potion of swiftness with longer duration. All this will do is update the current effect by making particles show and the potion icon show up in the HUD, but nothing else is modified including the duration of the current effect.
3. After the first effect runs out within 5 seconds, you no longer have any swiftness, thus you lost the effect of the potion you drank.

This issue relates to MC-169839.