Μην χάσεις τα χαρτιά σου, είναι στον φάκελο.

Μην is used for negative commands and negative wishes (i.e., “Don’t …”).
Δεν is used for ordinary negative statements (“not / don’t” in the sense of “I don’t…”).
So:

• Μην χάσεις… = Don’t lose… (command)
• Δεν χάνω… = I don’t lose… (statement)

Because after μη(ν) for “don’t …”, Greek typically uses the subjunctive form.
χάσεις is aorist subjunctive (2nd person singular) of χάνω (to lose). It often means “don’t let it happen (even once)” / “don’t end up losing.”
μην χάνεις would be present subjunctive, often implying “don’t be losing (repeatedly/continuously).” In many everyday contexts both can work, with a nuance:

• Μην χάσεις τα χαρτιά σου: don’t lose them (at all)
• Μην χάνεις τα χαρτιά σου: don’t keep losing them / don’t lose them habitually

• Dictionary form: χάνω = “to lose”
• χάσεις = aorist subjunctive, 2nd person singular
  It’s formed from the aorist stem χασ-
  • subjunctive ending -εις.

χαρτιά literally means “papers” and is very commonly used in the plural for documents, forms, or paperwork—similar to English “papers.”
Singular το χαρτί is “a (single) sheet of paper” or “a piece of paper.”

σου is the unstressed form of “your” (literally “of you”), used like a clitic genitive pronoun.
Greek normally puts these short possessives after the noun:

• τα χαρτιά σου = “your papers”
  You can also say τα δικά σου χαρτιά for emphasis: “your papers (not someone else’s).”

In Greek, neuter plural subjects often take a singular verb, especially in everyday usage:

• Τα χαρτιά σου είναι στον φάκελο. (verb form είναι is the same for singular and plural anyway, but the rule matters with other verbs too)

Example with a verb that shows number clearly:

• Τα παιδιά παίζουν. (children = not neuter)
• Τα βιβλία είναι εδώ. / (often treated as a collective set)

With είμαι, είναι is used for both “he/she/it is” and “they are,” so it doesn’t visibly change here.

στον is a contraction of σε + τον:

• σε = “in / to / at”
• τον = “the” (masculine accusative) So στον φάκελο literally means “in the folder.”

Similarly:

• στην = σε + την (feminine)
• στο = σε + το (neuter)
• στους / στις / στα = plural forms

φάκελο is accusative singular because the preposition σε takes the accusative:

• (σε) τον φάκελο → στον φάκελο
  Nominative would be ο φάκελος (“the folder” as a subject).

Yes. In Greek, χάνω τα χαρτιά μου can also be an idiom meaning “to lose track / get confused” (and in some contexts it can overlap with “lose your composure”).
But in your sentence, the follow-up είναι στον φάκελο (“they’re in the folder”) strongly pushes the literal meaning: actual papers/documents.

The comma separates two closely related clauses: 1) Μην χάσεις τα χαρτιά σου (command)
2) είναι στον φάκελο (explanation/reassurance)

Yes, Greek often links clauses like this with a comma. You could also make it two sentences:

• Μην χάσεις τα χαρτιά σου. Είναι στον φάκελο.

Yes, but it’s usually unnecessary because the context is clear:

• … είναι στον φάκελο. = “(They) are in the folder.”
  You might add αυτά for emphasis/clarity:
• … αυτά είναι στον φάκελο. = “Those are in the folder.” / “They’re in the folder.”

A rough guide (stress in CAPS):

• Μην ≈ meen
• χάσεις ≈ HA-sees
• τα ≈ ta
• χαρτιά ≈ har-TYA
• σου ≈ soo
• είναι ≈ EE-neh
• στον ≈ ston
• φάκελο ≈ FA-keh-lo