Summarized Changelog:

• Fix issue with dropping xlink:href attribute when collapsing referenced gradients.
• Fix issue with dropping ID while de-duplicating gradients.
• Improve --shorten-ids so it re-maps IDs that are already used in the document if they're shorter.
• Fix whitespace handling for SVG 1.2 flowed text.
• Improvement: Merge sibling <g> nodes with identical attributes.
• Improve performance of XML serialization.
• Improve performance of gradient de-duplication.
• Some general performance improvements.

• Save optimized SVG in Inkscape and then open again to see that it works.