The obvious way to avoid ambiguity (as to whether the other eclairs are also ours, or are made by the competition) is simply to repeat the subject of the verb1...
We keep our most popular available all year round, while others we rotate and change seasonally.
(That's also my added comma before while.)
1 Strictly speaking, the "subject" of the verb rotate in OP's original verb is others = other eclairs - but in context, ignoring the contrived ambiguity over who did the rotating (if it's not a "reflexive" act ascribed to the eclairs themselves), it would normally be fair to say that...
1: We rotate our eclair flavours every month
2: Eclair flavours are rotated every month
3: Eclair flavours rotate every month
...are equivalent in meaning (and are all idiomatic), regardless of the strict syntactic "verb subject".