Learn Swedish: Saxen som du klipper med saknas. - The scissors that you cut with are missing.

The preposition med shows the tool being used (the scissors). Just like in casual English, Swedish often leaves prepositions at the end of a relative clause. The phrase som du klipper med translates directly to 'that you cut with'.

Why is saxen translated as plural 'scissors' but treated as singular in the Swedish sentence?

In Swedish, a pair of scissors is a singular noun: en sax, and its definite form is saxen. Even though English treats 'scissors' as plural and uses a plural verb, Swedish treats the tool as a single object.

Could I say skär instead of klipper for 'cut'?

No, because Swedish uses different verbs for cutting depending on the tool. You use klipper when cutting with scissors (en sax) or shears. You use skär when slicing or cutting with a knife (en kniv).

Why does the verb saknas end in an -s?

It is an s-verb. Although the -s ending is often used to make verbs passive, saknas is a deponent verb. This means it has a passive form but an active meaning. Here, it simply means 'is missing'.