After writing all of this, I realised the issue is that all the blocks that no longer work are contained in a directory that contains a space in their name. After fixing that, the textures do now work. If this behaviour is intended, feel free to close this issue but otherwise I would appreciate a fix.

I have made a texture pack that connects a large number of different blocks, https://modrinth.com/resourcepack/its-all-connected. However, my issue is that when I was updating my pack from 1.21.1 to 1.21.4 over 2/3 of the textures stopped working.

(screenshot from 1.21.3, all of the blocks shown should be connected in 3x3 sections however only certain blocks like the barrel and lodestone are connected)

I tested on 1.21.1 with version 3.0.0+1.21 of continuity, version 0.114.0+1.21.1 of fabric api and fabric loader 0.16.9 (all of which should be the lastest versions). I then loaded in v1.1 of my texture pack as it has the reqired pack format number for that version, and all of the blocks in the image above were connected.

I then tested version 1.21.3 with version 3.0.0+1.21.3 of continuity, version 0.114.0+1.21.3 of fabric api and fabric loader 0.16.9. I then loaded both v1.1 and v1.2 of my texture pack and neither of them worked fully, both producing the image shown above. Similarly, I tested on 1.21.4 with those same mods and the same issue occured.

In this testing the only texture packs active are, from top to bottom, It's All Connected v1.1/v1.2, Fabric mods resources, and then the default textures. Additionally, I tested the default texture pack for continuity in all of these instances and in every case that pack worked fine.

Please also note that the beehive top texture in v1.2 of the pack will not work regardless, as I accidentally kept matchBlocks=beehive_end instead of matchTiles while trying to fix my issue. As a result of that testing, I found I could not fix any issues found by changing between matchBlocks and matchTiles, and similarly the working and non working blocks both use a mixture of matchBlock and matchTiles.

Here is the log file of testing on 1.21.3: latest.log
It seems to show the non working textures throw an "Invalid path in datapack" warning, however I am not sure how to resolve that issue.

Continuity for Minecraft 1.21.3 and newer no longer supports invalid resource location paths in any capacity, because OptiFine also removed this functionality recently. Spaces are not valid characters for resource location paths. Files located at an invalid path are treated by Minecraft as if they do not exist. For more information on resource locations, check this page on the Minecraft wiki.

Ok, thanks for the help!