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| then from September onwards we are on a C permit, so regular taxation until end of October (she didn't work in Nov and Dec). | |
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So she died

or left Switzerland

or got C revoked


If she was alive and in Switzerland with permit C she was also Nov and Dec on normal taxation.
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| (even though I applied for the extension before that date when the official papers came). [...] Is there really no way to do a retrospective reimbursement on QSt after the deadline of 31 March the following year has passed?! | |
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There is no procedure how you could request an extension for QSt recalculation. There is also no form they would send but you have to get it from them (
https://www.zh.ch/de/steuern-finanze...-personen.html ) and send it back to the tax office before March 31st (Canton YH, other cantons other dates).
If you want to have success you must make it clear that you thought in case of switching to permit C and to regular taxation the whole calendar year will be regularly taxed. Unfortunately, it is publicly known and clearly stated in §10 Quellensteuerverordnung I of Canton ZH
https://www.zh.ch/de/steuern-finanze...zstb-87-1.html that only from the month after one got permit C regular taxation is used.
Last straw if you are not successful with your plea is that the pro-rata income is more than 120k/year in which case regular taxation applies.