Notepad++ v8.1.6
URL Plugin v1.1.0.0

Decoding from percent-encoding to text works just fine.

• https://wiki.%E3%83%9D%E3%82%B1%E3%83%A2%E3%83%B3.com/ → decode:
• https://wiki.ポケモン.com/

Encoding results in a string that cannot be decoded. Here, I select just the ポケモン part and press Ctrl+Alt+Shift+E to encode. Alternatively, I select just the ポケモン part and select Plugins → URL Plugin → Encode URL.

• https://wiki.ポケモン.com/ → encode:
• https://wiki.%FFFFFFE3%FFFFFF83%FFFFFF9D%FFFFFFE3%FFFFFF82%FFFFFFB1%FFFFFFE3%FFFFFF83%FFFFFFA2%FFFFFFE3%FFFFFF83%FFFFFFB3.com/

Attempting to decode the above results in a mess.

• https://wiki.%FFFFFFE3%FFFFFF83%FFFFFF9D%FFFFFFE3%FFFFFF82%FFFFFFB1%FFFFFFE3%FFFFFF83%FFFFFFA2%FFFFFFE3%FFFFFF83%FFFFFFB3.com/ → decode:
• https://wiki.ÿFFFFE3ÿFFFF83ÿFFFF9DÿFFFFE3ÿFFFF82ÿFFFFB1ÿFFFFE3ÿFFFF83ÿFFFFA2ÿFFFFE3ÿFFFF83ÿFFFFB3.com/

If I first apply a regex to remove all instances of FFFFFF, decoding can succeed.

• https://wiki.%FFFFFFE3%FFFFFF83%FFFFFF9D%FFFFFFE3%FFFFFF82%FFFFFFB1%FFFFFFE3%FFFFFF83%FFFFFFA2%FFFFFFE3%FFFFFF83%FFFFFFB3.com/ → regex to remove FFFFFF:
• https://wiki.%E3%83%9D%E3%82%B1%E3%83%A2%E3%83%B3.com/ → decode:
• https://wiki.ポケモン.com/

Suggestion:

The encoding feature should not prepend FFFFFF.