Is the validator error saying that the phase-difference file is missing the EchoTime1 and EchoTime2 metadata fields? If so, then the that information should be available somewhere. What do the phase-difference and magnitude files have for their standard EchoTime fields?
EDIT: I see that this issue is linked to Converting Philips Fieldmaps to BIDS and finding Echo time 1 and Echo time 2, in which you say that the echo times for both the phase-difference and magnitude images are 0.0032.
I noticed that the PAR/REC metadata included delta TE (ms) = 1;, which would indicate to me that the second echo time is 4.2 ms (since we know that 3.2 ms is the shortest TE). However, I need to warn you that I have zero experience with PAR/REC files or Philips data in general, so you should take that with a big grain of salt. I didn’t read the other topic in detail, but I did see that @Chris_Rorden responded there. If he has something different to say about the issue, then I’d trust him.