This does not apply to Yom Kippur as there is no kiddush to be mafseik. The women should not say the shechiyanu in Shul after kol nidrei if they have already said on the candles. Where is the source for this?
You could find it in the Kitzur Shulchan Aruch (132:2)
כְּשֶׁשְּׁלִיחַ הַצִּבּוּר אוֹמֵר בִּרְכַּת שֶׁהֶחֱיָנוּ, יְכַוֵּן לְהוֹצִיא אֶת הַצִּבּוּר. וּמִכָּל מָקוֹם נָכוֹן שֶׁהַשּׁוֹמֵעַ יְכַוֵּן שֶׁלֹּא יֵצֵא בְּבִרְכַּת שְּׁלִיחַ הַצִּבּור, אֶלָּא יְבָרֵךְ בְּעַצְמוֹ בְּלַחַשׁ, וִימַהֵר לְסַיֵם קֹדֶם שְּׁלִיחַ הַצִּבּור, כְּדֵי שֶיַעֲנֶה אָמֵן. וְהַנָּשִׁים שֶבֵּרְכוּ בְּהַדְלָקַת הַנֵּרוֹת שֶׁהֶחֱיָנוּ, וְכֵן אִישׁ אִם הִדְלִיק וּבֵרַךְ אָז שֶׁהֶחֱיָנוּ, לֹא יְבָרְכוּ עַתָּה שֶׁהֶחֱיָנוּ (סִימָן תריט, ובסידור בשם מטה אפרים).
Earlier you stated:
On Yom Tov women light candles and make a shechiyanu. They may not answer אמן to their husband’s berachah of shechiyanu at kiddush because that would be a hefseik in the woman’s kiddush. Alternatively, she may skip the shechiyanu at candle lighting, answer אמן at kiddush and have in mind the candles as well.
As for your assertion that
They may not answer אמן to their husband’s berachah of shechiyanu at kiddush because that would be a hefseik in the woman’s kiddush..
The Aruch HaShulcan (263:12) states that some make the שהחיינו but does not mention that they should not answer אמן to their husband’s Brachah of שהחיינו at Kiddush:
ונשים שלנו מברכות גם 'שהחיינו' בעת הדלקת הנרות ביום טוב, ואין למחות בידן, דעל פי רוב בערב יום טוב מדליקות לעת ערב ממש, וקאי 'שהחיינו' על יום טוב. ויש מפקפקים בזה, והנח להן לבנות ישראל מנהגן. וביום הכיפורים יש מברכין ויש שאין מברכין, ואנחנו נהגנו לברך ויתבאר בסימן תר''י ע''ש.
See Ask the Rabbi Women Answering Amen to Schehechayanu in Kiddush whre this is discussed by Rabbi Yoel Lieberman who brings many sources - for and against this opinion. Here's a copy:
In regard to the "Hefsek" for women who have said Shehechiyanu, see Shmirat Shabbat Kehilchata Vol.II, Chap. 44:4, note 17.
The Mishna B'rura (סימן רסג ס"ק כג) actually suggests that women refrain from saying Shehechiyanu by candle lighting. This is based on the She'ilat Yaavetz who said there is no source for this practice, but he also says that women who do so should not be rebuked. After having said Shehechiyanu at candle lighting, they should therefore not answer Amen to the Shehechiyanu by Kiddush since it constitutes an interruption. (See Shmirat Shabbat Kehilchata Vol.II, Chap. 44:4).
However, as known in many households saying Shehechiyanu at candle lighting has been the practice for many generations and it appears in many siddurim. Now the question arises do we tell them to stop the practice and do start telling women not to say amen after a "bracha".
The She'ilat Yaavetz 107 said he did not stop his wife from saying Shehechiyanu at candle lighting.
Rav Moshe Feinstein zt"l (אגרות משה או"ח ח"ד, קא ) says that the women answering "amen" after Shehechiyanu at Kiddush is not a "hefsek" for this has been the practice for hundreds of years and would it actually be a hefsek women should have been rebuked and told to discontinue. Furthermore, he says that telling people not to say amen can be detrimental. (See also שו"ת רבבות אפרים ח"א סי' קפב ) On the other hand, Rav Feinstein zt"l also says where there is no such practice women should begin to do so.
In Luach Eretz Yisrael of Rav Tokatchinsky zt"l that women say Shehechiyanu at candle lighting. Although, he does quote the reservation of the above Ya'avetz in parenthesis, he did not forbid the practice.
The Aruch Hashulchan 263:12 also says that the practice of our women is to Shehechiyanu at candle lighting and they are not to be rebuked since they usually light the candles right before Yom Tov and the Shehechiyanu is meant for the Yom tov and not the candle lighting.
However, Rav Ovadia Yoseph Shlit"a in Yechaveh Da'at 3:34 rules that women should discontinue the practice of Shehechiyanu at candle lighting.