I was having the same issue and it was driving me crazy. You need to add yellow to the macro before removing the {% if annotation.color !== "#ffd400" %} line of code. Honestly I messed with the template a lot, so there may have been other minor tweaks.
Here is my working template:
## Annotations
{% macro calloutHeader(color) -%}
{%- if color == "#a28ae5" -%}
Highlight - Purple
{%- endif -%}
{%- if color == "#2ea8e5" -%}
Reference to Read - Blue
{%- endif -%}
{%- if color == "#5fb236" -%}
Key Information - Green
{%- endif -%}
{%- if color == "#ff6666" -%}
Question - Red
{%- endif -%}
{%- if color == "#ffd400" -%}
Important - Yellow
{%- endif -%}
{%- endmacro -%}
{% persist "annotations" %}
{% set annotations = annotations | filterby("date", "dateafter", lastImportDate) -%}
{% if annotations.length > 0 %}
#### Imported on {{importDate | format("YYYY-MM-DD h:mm a")}}
{%- for annotation in annotations %}
> [!quote{% if annotation.color %}|{{annotation.color}}{% endif %}] {{calloutHeader(annotation.color)}}
{%- if annotation.imageRelativePath %}
> ![[{{annotation.imageRelativePath}}]]
{%- endif %}
{%- if annotation.annotatedText %}
>{{annotation.annotatedText}} [(p. {{annotation.pageLabel}})](zotero://open-pdf/library/items/{{annotation.attachment.itemKey}}?page={{annotation.pageLabel}}&annotation={{annotation.id}}){%- endif %}
{%- if annotation.comment %}
>
>> {{annotation.comment | nl2br}}{%- endif %}
{% endfor -%}
{% endif %}
{% endpersist %}
And this is what it looks like:
