From: Rabbi Moshe Sofer
To: Unknown recipient
The Chasam Sofer rules that mixing Rashi's and Rabbeinu Tam's styles of ches within one Sefer Torah does not constitute a prohibited internal contradiction (tartei d'sasrei). However, erasing the widened ches letters may involve horadah mikdusha, since the Malbushei Yom Tov holds they are valid according to Rabbeinu Tam. Practically, he advises using another Sefer Torah if available, relying on the Malbushei Yom Tov in pressing circumstances, or ideally cutting out the problematic section and patching it with properly written letters.
Source: Shu"t Chasam Sofer YD §258