diff --git a/include/gfx/main.hpp b/include/gfx/main.hpp
index 1a0fb6d5..15128aaa 100644
--- a/include/gfx/main.hpp
+++ b/include/gfx/main.hpp
@@ -73,6 +73,8 @@ struct Palette {
 	decltype(colors)::iterator end();
 	decltype(colors)::const_iterator begin() const;
 	decltype(colors)::const_iterator end() const;
+
+	uint8_t size() const;
 };
 
 #endif /* RGBDS_GFX_MAIN_HPP */
diff --git a/src/gfx/main.cpp b/src/gfx/main.cpp
index c1dc3c29..d2ec1eb5 100644
--- a/src/gfx/main.cpp
+++ b/src/gfx/main.cpp
@@ -374,7 +374,7 @@ void Palette::addColor(uint16_t color) {
 }
 
 uint8_t Palette::indexOf(uint16_t color) const {
-	return std::distance(colors.begin(), std::find(colors.begin(), colors.end(), color));
+	return std::find(colors.begin(), colors.end(), color) - colors.begin();
 }
 
 auto Palette::begin() -> decltype(colors)::iterator {
@@ -390,3 +390,7 @@ auto Palette::begin() const -> decltype(colors)::const_iterator {
 auto Palette::end() const -> decltype(colors)::const_iterator {
 	return std::find(colors.begin(), colors.end(), UINT16_MAX);
 }
+
+uint8_t Palette::size() const {
+	return indexOf(UINT16_MAX);
+}
diff --git a/src/gfx/pal_sorting.cpp b/src/gfx/pal_sorting.cpp
index 756746ee..0ce543fa 100644
--- a/src/gfx/pal_sorting.cpp
+++ b/src/gfx/pal_sorting.cpp
@@ -10,27 +10,56 @@
 #include "gfx/convert.hpp"
 #include "gfx/main.hpp"
 
+using std::swap;
+
 namespace sorting {
 
 void indexed(std::vector<Palette> &palettes, int palSize, png_color const *palRGB,
              png_byte *palAlpha) {
 	options.verbosePrint("Sorting palettes using embedded palette...\n");
 
+	auto pngToRgb = [&palRGB, &palAlpha](int index) {
+		auto const &c = palRGB[index];
+		return Rgba(c.red, c.green, c.blue, palAlpha ? palAlpha[index] : 0xFF);
+	};
+
+	// HACK: for compatibility with old versions, add unused colors if:
+	// - there is only one palette, and
+	// - only some of the first N colors are being used
+	if (palettes.size() == 1) {
+		Palette &palette = palettes[0];
+		// Build our candidate array of colors
+		decltype(palette.colors) colors{UINT16_MAX, UINT16_MAX, UINT16_MAX, UINT16_MAX};
+		for (int i = 0; i < options.maxPalSize(); ++i) {
+			colors[i] = pngToRgb(i).cgbColor();
+		}
+
+		// Check that the palette only uses those colors
+		if (std::all_of(palette.begin(), palette.end(), [&colors](uint16_t color) {
+				return std::find(colors.begin(), colors.end(), color) != colors.end();
+			})) {
+			if (palette.size() != options.maxPalSize()) {
+				warning("Unused color in PNG embedded palette was re-added; please use `-c embedded` to get this in future versions");
+			}
+			// Overwrite the palette, and return with that (it's already sorted)
+			palette.colors = colors;
+			return;
+		}
+	}
+
 	for (Palette &pal : palettes) {
 		std::sort(pal.begin(), pal.end(), [&](uint16_t lhs, uint16_t rhs) {
 			// Iterate through the PNG's palette, looking for either of the two
 			for (int i = 0; i < palSize; ++i) {
-				auto const &c = palRGB[i];
-				Rgba color(c.red, c.green, c.blue, palAlpha ? palAlpha[i] : 0xFF);
-				uint16_t cgbColor = color.cgbColor();
-				if (cgbColor == Rgba::transparent) {
+				uint16_t color = pngToRgb(i).cgbColor();
+				if (color == Rgba::transparent) {
 					continue;
 				}
 				// Return whether lhs < rhs
-				if (cgbColor == rhs) {
+				if (color == rhs) {
 					return false;
 				}
-				if (cgbColor == lhs) {
+				if (color == lhs) {
 					return true;
 				}
 			}
diff --git a/test/pokecrystal.patch b/test/pokecrystal.patch
deleted file mode 100644
index 6f85efb4..00000000
--- a/test/pokecrystal.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff --git a/Makefile b/Makefile
-index ca08f23f..abd2e95c 100644
---- a/Makefile
-+++ b/Makefile
-@@ -170,9 +170,9 @@ gfx/pokemon/girafarig/front.animated.tilemap: gfx/pokemon/girafarig/front.2bpp g
- 
- ### Misc file-specific graphics rules
- 
--gfx/pokemon/%/back.2bpp: rgbgfx += -h
-+gfx/pokemon/%/back.2bpp: rgbgfx += -h -c embedded
- 
--gfx/trainers/%.2bpp: rgbgfx += -h
-+gfx/trainers/%.2bpp: rgbgfx += -h -c embedded
- 
- gfx/pokemon/egg/unused_front.2bpp: rgbgfx += -h
- 
diff --git a/test/run-tests.sh b/test/run-tests.sh
index b0358da0..85953ade 100755
--- a/test/run-tests.sh
+++ b/test/run-tests.sh
@@ -30,8 +30,7 @@ if [ ! -d pokecrystal ]; then
 fi
 pushd pokecrystal
 git fetch
-git checkout a3e31d6463e6313aed12ebc733b3f772f2fc78d7 -f
-git apply ../pokecrystal.patch
+git checkout a3e31d6463e6313aed12ebc733b3f772f2fc78d7
 make clean
 make -j4 compare RGBDS=../../
 popd