I have identified 61 Mutopia entries that have invalid unicode encodings. In the alphabetical list below, I have broken the list up into blocks of a reasonable size in the event anyone would like to participate in this update. Each line is a single Mutopia index but some entries are folders that may contain more than one lilypond file.
Most editors can make the conversion, but almost all of them need to updated to a more current version of lilypond anyway and running convert-ly will also make the encoding fix.
Block 1.
BachJS/BWV1050/brand5-3
BachJS/BWV269/bwv_269
BachJS/BWV347/bwv347
BachJS/BWV803/duetto
BachJS/BWV846/wtk1-fugue1
BachJS/BWV928/prelude_9
BachJS/O_Haupt_voll_Blut/O_Haupt_voll_Blut.ly
Block 2:
[ COMPLETE ] BeethovenLv/O62/Coriolan
BrahmsJ/O118/intermezzo
ChopinFF/O10/10-02-i
ChopinFF/O10/chopin-op-10-09-wfi
ChopinFF/O10/op-10-12-wfi
ChopinFF/O25/chopin-op-25-01
ChopinFF/O28/Chop-28-2
ChopinFF/O69/w10-h-moll-cfi
[ SKIP ] DandrieuJ/Fugue_sur_l_Ave_maris_stella/Fugue_sur_l_Ave_maris_stella.ly
GrignyNd/Grigny-Fugue_a_5/Grigny-Fugue_a_5.ly
[ COMPLETE ] Block 3.
[ COMPLETE ] HandelGF/Aylesford/01-overture
[ COMPLETE ] HandelGF/Aylesford/02-entree
[ COMPLETE ] HandelGF/Aylesford/03-gavotte
[ COMPLETE ] HandelGF/Aylesford/04-toccata
[ COMPLETE ] HandelGF/Aylesford/05-fuga
[ COMPLETE ] HandelGF/Aylesford/06-impertinence
[ COMPLETE ] HandelGF/Aylesford/07-concerto
[ COMPLETE ] HandelGF/Aylesford/08-preludio
[ COMPLETE ] HandelGF/Aylesford/09-menueti
[ COMPLETE ] HandelGF/Aylesford/10-menuetii
[ COMPLETE ] HandelGF/Aylesford/11-allegro
[ COMPLETE ] HandelGF/Aylesford/12-menuet
[ COMPLETE ] HandelGF/Aylesford/13-air
[ COMPLETE ] HandelGF/Aylesford/14-menueti
[ COMPLETE ] HandelGF/Aylesford/15-menuetii
[ COMPLETE ] HandelGF/Aylesford/16-airmitvar
[ COMPLETE ] HandelGF/Aylesford/17-allemande
[ COMPLETE ] HandelGF/Aylesford/18-passepied
[ COMPLETE ] HandelGF/Aylesford/19-menuet
Block 4.
KuhlauF/O20/sonatine-1-allegro
KuhlauF/O20/sonatine-1-andante
LullyJB/LWV71/Armide
Mendelssohn-BartholdyF/O36/paulus_3
Mendelssohn-BartholdyF/O70/elias_32
MozartWA/KV574/k574
RameauJP/sauvages/sauvages.ly
SchubertF/D118/gretchen
SchubertF/D550/forelle
SchubertF/D911/einsamkeit
Block 5.
SchulzJAP/mond/mond.ly
SchumannR/O48/Ich_grolle_nicht
SorF/O1/sor_op_1_4
SorF/O1/sor_op_1_5_1
SorF/O1/sor_op_1_5_2
SorF/O1/sor_op_1_5_3
SorF/O1/sor_op_1_6
SorF/O60/sor_op60-03
SorF/O60/sor_op60-05
Block 6.
TitelouzeJ/Ave_Maris_Stella-1er_verset/Ave_Maris_Stella-1er_verset.ly
TitelouzeJ/Ave_Maris_Stella-3e_verset/Ave_Maris_Stella-3e_verset.ly
TitelouzeJ/Ave_Maris_Stella-4e_verset/Ave_Maris_Stella-4e_verset.ly
TitelouzeJ/Pange_Lingua-2e_verset/Pange_Lingua-2e_verset.ly
TitelouzeJ/Veni_Creator-1er_verset/Veni_Creator-1er_verset.ly