Here is a comment about that: TWRP for Fairphone 3 - #262 by _tmp
Basically, your phone has several different partitions called boot, modem, system etc (the post above the one I linked shows a script with all the important partitions and their names). Old updates had .img files with the corresponding names for those partitions.
However, there’s a new standard of naming partitions and Fairphone updates adhere to that - .mbn files, .bin files etc. Your phone doesn’t adhere to this standard as it is older, so one has to “translate” the new file names to the old ones. The file “partition.txt” does exactly this, it matches the old partition name standard to the new one.
What your flashall.exe does is basically just booting into fastboot and then executing all those commands like “fastboot flash modem_a modem.img”. Just instead of flashing a file originally called “modem.img” it flashes the corresponding newly named file “NON-HLOS.bin”. But you can do all this manually if you want to, if you look up the file names in partition.txt. Or, if you’re like me, you can copy and rename all those files to their old names and then flash them in the right order, This helps me make sure if have everything and didn’t forget something.
Frankly, even though I’m by no means an expert in this stuff but rather a rookie, I have a feeling that your modem partitions might have the wrong size or something, they don’t get flashed correctly and that’s why your phone doesn’t boot properly.