The main verb of the second clause

Solution 1:

Not only is the verb missing from the second clause, so is the Subject.

They are deleted by the rule of Conjunction Reduction, which has been applied to two conjoined clauses, deleting the (repeated) subject and auxiliary be.

Stripped of modificational bells and whistles, the original compound sentence is

• The power source is not a nuclear reactor
  but rather
  the power source is a nuclear battery.

and the second occurrence of the power source is gets deleted because it's predictable.
producing the compound Verb Phrase

• is not a nuclear reactor but a nuclear battery

Solution 2:

The second verb in the clause beginning with 'but' is the implied verb 'is'.

You could rephrase the sentence as:

The energy source on Voyager2 is not a nuclear reactor, in which atoms are actively broken apart, but is rather a kind of nuclear battery that uses natural radioactive decay to produce power.