Learn French: Le projet est moins compliqué et coûteux que je ne le croyais. - The project is less complicated and costly than I believed.

This is the ne explétif (expletive ne), the main focus of your current lesson. It does not mean 'not.' In formal or careful French, it is often added after affirmative comparisons of inequality (using words like plus or moins). It simply highlights the gap between reality and expectation. It is not translated into English, and leaving it out in casual spoken French is completely fine.

What exactly does the le in que je ne le croyais refer to?

This is the neutral pronoun le. Instead of replacing a specific masculine noun, it stands in for an entire idea or state of being—in this case, being 'complicated and costly.' While in English we simply say 'than I believed,' French prefers to explicitly reference the concept: 'than I believed it (to be).'

Why use the imperfect tense (croyais) here instead of the passé composé (ai cru)?

The imperfect is used because it describes an ongoing state of mind in the past. Your belief that the project was highly complicated and costly was a continuous background thought before you realized the truth. The passé composé is reserved for sudden, completed actions, which does not fit a prolonged state of belief.

Do I need to repeat moins and say moins compliqué et moins coûteux?