Ghost 4/4 measure?

The entire piece I'm transcribing/fixing is in 3/4. For more context, I used the PDF converter, and other than a few minor/annoying errors, the piece came out pretty fine. That is until bar 55, where the time signature switches to 4/4 with no markings. Every bar afterwards is fine, back in 3/4. If I manually add a 3/4 to the bar, nothing happens, but if I remove the new 3/4, the bar's finally in 3/4, but to coincide with the ghost 4/4, the entire piece shifts one beat over.

File 1: The ghost 4/4 bar.
File 2: Removing the manually placed 3/4.