Ran some checks to see how many @sameAs attributes are not pointing at existing @xml:ids. There are 160 cases where the @sameAs has a value (is not empty), but there's no corresponding @xml:id on an entry:

skʷtas in entry skWtas
kn in entry kascaʔqWmixn
lqs in entry scəslqs
lqs in entry scəslqs
nwˀáln in entry cx̣cx̣nwˀalnˀ
sac in entry saṣc̣ụṣkṣtəxW
n-LOC in entry naḥaʔe
m-MID in entry ḥacm
OC in entry ḥacc
k-LOC in entry kḥacn
min-INST in entry ḥacmin
t-TR in entry ḥacpnuntn
OC in entry ḥacḥacc
n-LOC in entry nḥacawˀsn
min-INST in entry ḥacmintn
tn in entry ḥacmintn
kɬ-LOC in entry kɬḥacmintn
min-INST in entry kɬḥacmintn
tn in entry kɬḥacmintn
n-LOC in entry naḥcusmn
min-INST in entry naḥcusmn
n-LOC in entry naḥcapxn
ap in entry naḥcapxn
k-LOC in entry kḥac̣ḥac̣qinˀxn
CHAR in entry kḥac̣ḥac̣qinˀxn
tn in entry ḥacʼxWn
ḥaḥənt in entry sḥaḥəntaɬxW
ḥalˀxʷ in entry kasḥalˀxWmíx
ḥalˀxʷ in entry ḥalˀxWn
n-LOC in entry naḥalˀxW
ḥalˀxʷ in entry naḥalˀxW
ḥalˀxʷ in entry ḥalˀxWulˀəxW
ḥalˀxʷ in entry ḥalˀḥalˀxWxn_kn
kn in entry ḥalˀḥalˀxWxn_kn
kn in entry kn_ḥalˀḥalˀxWxn
ḥalˀxʷ in entry kn_ḥalˀḥalˀxWxn
kn in entry kn_tḥalˀḥalˀxWanaʔ
t-LOC in entry kn_tḥalˀḥalˀxWanaʔ
ḥalˀxʷ in entry kn_tḥalˀḥalˀxWanaʔ
t-LOC in entry tḥaƛʼm
OC in entry ḥaƛʼƛʼ
OC in entry sḥaƛʼƛʼ
OC in entry sḥaƛʼƛʼtn
tn in entry sḥaƛʼƛʼtn
OC in entry ḥaƛʼƛʼcin
OC in entry sḥaƛʼƛʼnus
OC in entry ḥaƛʼƛʼamˀinˀaʔ
kat in entry katḥaƛʼƛʼanaʔ
OC in entry katḥaƛʼƛʼanaʔ
ʔin in entry ʔiscḥamcin
sac in entry ʔiscḥamcin
limt in entry ḥamlimt
kn in entry kn_ḥamlimt
limt in entry kn_ḥamlimt
OC in entry ḥamm
n-SUBJ in entry ḥamˀcn
n-SUBJ in entry ḥamˀn_lx
t-TR in entry ḥamˀntm_lx
OC in entry ḥassus
CHAR in entry ḥatḥat
n-LOC in entry snḥawaɬcʼaʔtn
tn in entry snḥawaɬcʼaʔtn
ayˀ-PAST in entry kasḥawˀiɬtmnayˀuxW
ayˀ-PAST in entry sḥawˀiɬtmnayˀm
m-MID in entry sḥawˀiɬtmnayˀm
sac in entry scḥawˀi
sac in entry scḥawˀiymix
kn in entry kn_ḥawˀiyasnccwˀaxaʔ
sac in entry scḥawˀiymix_lx
kn in entry kn_scḥawˀiymix
sac in entry kn_scḥawˀiymix
sac in entry scḥawˀiymix_kt
sac in entry scḥawˀiymix_kW
sac in entry scḥawˀiymix_kWp
m-MID in entry ḥawˀiym
m-MID in entry sḥawˀiym
n-SUBJ in entry kasḥawˀiyn
t-TR in entry ḥawˀiyntxW
xW-SUBJ in entry ḥawˀiyntxW
n-SUBJ in entry ḥawˀiyminn
n-SUBJ in entry ḥawˀiyminnayˀ
ayˀ-PAST in entry ḥawˀiyminnayˀ
n-SUBJ in entry ḥawˀiyminn_lx
n-SUBJ in entry cḥawˀiystunn
ɬ-DIR in entry cḥawˀiɬtunn
n-SUBJ in entry cḥawˀiɬtunn
ɬ-DIR in entry ḥawˀiɬt-2
t-TR in entry ḥawˀiɬt-2
t-SUBJ in entry ḥawˀiɬt-2
ɬ-DIR in entry ḥawˀiɬt-2
t-TR in entry ḥawˀiɬt-2
n-SUBJ in entry ḥawˀiyxitn
n-SUBJ in entry cḥawˀixitn
ʔin in entry ʔiscḥawˀi
sac in entry scḥawˀiys
s-POSS in entry scḥawˀiys
n-SUBJ in entry ʔalḥawˀiyn
sac in entry scḥawˀiyaltuxW
m-MID in entry ḥawˀiyaltm
sac in entry scḥawˀiyaɬxWuxW
kn in entry kn_ḥawˀiyáɬxW
m-MID in entry ḥawˀiyaɬxWm
m-MID in entry ḥawˀiylupm
min-INST in entry ḥawˀiymin
min-INST in entry ḥawˀiyminn-2
ham in entry chamhamilx
CHAR in entry chamhamilx
kn in entry kn_hamp
kn in entry kn_hampncut
n-LOC in entry nahamp
CHAR in entry hamhampul
n-LOC in entry nhampatkW
k-LOC in entry khamhampawˀs
k-LOC in entry khamhampakstmn
m-MID in entry hampmnatkWmˀ
m-MID in entry hampmnatkWmˀ
wil in entry hapyˀwil
wil in entry hapyˀwil
m-MID in entry hapyˀwil
n-LOC in entry nhapyˀatkWn
kn in entry kn_sḥaypx̣əxW
OC in entry hə̣ll
t-TR in entry huymn
ayʼ in entry huymnayʼ
t-TR in entry chuymntls
Ø-OBJ m-SUBJ in entry huystm
m-OBJ in entry ʔachuymstms
ɬ-DIR in entry huyɬn
Ø-OBJ n-SUBJ in entry huyɬn
ɬ-DIR in entry kashuyɬn
Ø-OBJ n-SUBJ in entry kashuyɬn
n-LOC in entry nahuyxn
CHAR in entry sʕWaʔʕWaʔ
CHAR in entry sʕWʕWaʔʕWaʔ
askʼayˀt in entry ʕWəcʼpaskʼayˀt
kat in entry katʕWətʼqWatkW
ups in entry ʕˀWənˀps
ups in entry ʕˀWənʕˀWanps
n-LOC in entry nʕˀWənˀʕˀWanˀpsn
ups in entry nʕˀWənˀʕˀWanˀpsn
tn in entry nʕˀWənˀʕˀWanˀpsn
CHAR in entry sʕˀWəsʕˀWəs
CHAR in entry sʕˀWəsʕˀWəs
CHAR in entry sʕˀWʕˀWəsʕˀWəs
niʔ in entry niʔqʼWacʼlqs
n-LOC in entry naqʼWacʼt
kn in entry kn_qʼWqʼWacʼltn
tn in entry kn_qʼWqʼWacʼltn
kn in entry kn_qʼWəcʼqʼWacʼltn
tn in entry qʼWəcʼqʼWacʼltn_lx
OC in entry qʼWalˀlˀx
m-MID in entry qʼWaɬtmm
CHAR in entry sanspax̣pax̣t
CHAR in entry ṣə̣nṣə̣nt
CHAR in entry ṣə̣nṣə̣nt_lx
CHAR in entry ṣə̣nṣə̣ntwilˀx
OC in entry ṣụʔụʔtʼ
niʔ in entry niʔṣụʔṣụʔtḷqs
lqs in entry niʔṣụʔṣụʔtḷqs
solcas in entry ṣolcaṣ 

Most of these will be expected, but some may be typos.