The relative converter ⲉⲧ is not considered referential. In relative clauses with explicit subject pronouns, those pronouns are annotated as usual:
ⲙ [ⲡ ⲙⲁ ⲉⲧ [ϥ] ⲛϩⲏⲧ [ϥ]] - The place that he is in (it)
Note that this results in the second pronoun pointing back to the span that contains it - this is allowed in WebAnno.
Correlative/expletive pronouns are not annotated as entities at all:
In morphologically complex items containing a verb inside a larger token, that noun cannot be annotated: