Although it might be a bit slow, I found a solution by manually deleting and adding in the file. I'll leave the code here in case anyone else comes across this problem.
ZipFile zipnew = new ZipFile(forgeFile);
ZipFile zipold = new ZipFile(zFile);
using(zipnew) {
// Loop through each entry in the zip file
foreach(ZipEntry zenew in zipnew) {
string flna = zenew.FileName;
// Create a new memory stream for extracted files
var ms = new MemoryStream();
// Extract entry into the memory stream
zenew.Extract(ms);
ms.Seek(0, SeekOrigin.Begin); // Rewind the memory stream
using(zipold) {
// Remove existing entry first
try {
zipold.RemoveEntry(flna);
zipold.Save();
}
catch (System.Exception ex) {} // Ignore if there is nothing found
// Add in the new entry
var zn = zipold.AddEntry(flna, ms);
zipold.Save(); // Save the zip file with the newly added file
ms.Dispose(); // Dispose of the stream so resources are released
}
}
zipnew.Dispose(); // Close the zip file
}