The full line looks like not implemented: secondary decompressor (id=N). N is a number, not a ROM region. VCDIFF allows a secondary compressor on the window data. xdelta3 turns that on with -S. Its names are lzma, fgk, djw, and none. In the source I read, the option defaults on when LZMA is compiled in. A patch from a current xdelta3 is therefore likely to carry that layer. An older browser decoder that only understands raw windows stops and prints this sentence.
The module pinned here, commit 4f17297 from 21 Oct 2026, handles two ids. Id 1 is DJW static Huffman. Id 2 is LZMA. The commit message is that LZMA decoding was added. If your id is 1 or 2 and you still see the message, you are not on this commit. The v3.2.1 tag is older than that commit. The v3.5 label on the author's hosted page is a different string again. I do not promise that label includes this decoder. I promise the commit hash.
If the id is something else, this decoder will still refuse. The author's fix is to rebuild the patch with xdelta3 -S none so the windows are plain. That is a new file the patch author should publish. Stripping headers, swapping N64 byte order, or changing FireRed revisions will not remove a compressor. Those are other errors with other sentences.
Large DS, GameCube, and PS2 patches are where this shows up, because that is where xdelta is the format. Related pages: the xdelta guide and Delta Patcher, which is where a creator can see the compressor setting. The error index lists the checksum messages so you can tell them apart.