إِنَّ هَذَا السِّجِلَّ ـ وَاللَّهُ يَعْلَمُ صِدْقَ النِّيَّاتِ ـ يَحْفَظُ مَا شَاهَدْنَاهُ.
This record—God knows the sincerity of intentions—preserves what we observed.
The governing predication runs from inna hādhā al-sijilla to yaḥfaẓu. The inserted independent clause comments on sincerity but is not necessary to complete that syntactic structure. It can be analyzed as iʿtirāḍ, a parenthetic addition.
Quotation marks or dashes alone do not make a passage parenthetic in the technical sense. The relevant issue is an extra sentence inserted between closely related parts of the ongoing construction.