"She does not want to assume that he does not like her."
Translation:Hun vil ikke anta at han ikke liker henne.
Can someone explain the word order in the second half? How flexible is it?
I dont think it is very flexible. The subject has too come first because it is after a conjunction. Next the adverb(s) because it is a dependent clause. Then the verb. And finally the object. So the order for dependent clauses is: Subject adverb verb object
when it comes to "ikke liker" VS "liker ikke", how is their usage different?
You can try counter-translating it; ie. "She doesn't want to assume that he doesn't like her" --> "Hun vil ikke anta at han ikke liker henne." vs "She doesn't want to assume that he like doesn't her" --> "Hun vil ikke anta at han liker ikke henne".
Could henne be replaced with sine - assuming the subject is referring to herself?