After rebuilding content not able to see

Problem/Motivation

Domain Simple Sitemap + Simple Sitemap: this can generate per-domain sitemaps, but:
If I don’t rebuild permissions, the sitemap jobs stay in pending state.
If I do rebuild permissions, new content shows up fine, but old content is not visible to assigned users (even after granting all likely permissions). Old nodes exist but don’t appear for the microsite users.

Is there a safe way to regenerate node/domain access so old content becomes visible again (without breaking permissions/visibility), or any steps to restore domain assignments after a rebuild?
Alternatives: should we switch to path-based sitemaps (xmlsitemap variants / custom sitemap per path) or write a small custom sitemap generator for each microsite? Any recommendations?