Situations Where Characters Can Lose Checkmarks

• Characters can sometimes be instructed to lose checkmarks. The rulebook does not specify all possible sources for this instruction, but it acknowledges that such situations can occur.

Effect on Perk Marks and Perks Already Gained

• Perk marks cannot be lost. If a character is instructed to lose checkmarks, they can only lose checkmarks back to the last complete set of three.
  • Example: If a character has eight checkmarks, they can lose up to two checkmarks, but no more. This is because perk marks are gained for each complete set of three checkmarks, and once a perk mark is gained, it cannot be lost.
• Perks already gained remain. Since perk marks cannot be lost, any perks that were gained by spending those perk marks are also permanent and cannot be lost, even if checkmarks are lost later.

Source: page 63

This answer is based on the following excerpt:

Sometimes, a character will be instructed to lose checkmarks. However, perk marks cannot be lost, so checkmarks can only be lost back to the last complete set of three checkmarks. For example, if a character has eight checkmarks, it is possible for them to lose up to two checkmarks, but no more.

Source: Core Rulebook (pp. 17, 47, 48, 55, 63)