Hello,
How did you generate the PDF files you're merging? We recommend you to embed the fonts into the PDF documents before merging it. Other approach is to install the needed fonts in the OS that are generating the PDF.
Phpdocx uses TCPDF and FPDI to merge PDF files. You can change their default values such as the helvetica font family in the lib folder of the package.
The current version of phpdocx doesn't include an option to change these default values but we've added a task to include it in a next version of the library.
Regards.