From: Rabbi Moshe Sofer
To: Rabbi Chaim
The Chasam Sofer rules stringently regarding letters that span both the original parchment and a patch, disqualifying such a Sefer Torah from use. However, where entire letters are written wholly on a patch, established custom permits it. The remedy is to remove defective patches and replace them so all letters fall entirely on the new patches, and such a corrected Sefer Torah is not disqualified for appearing menumar.
Source: Shu"t Chasam Sofer YD §278