How do I batch convert 3MF files without losing the original print settings?

It reads each file on its own, so you're safe there. I ran a mixed batch of about fifteen models thru it a while back, all from diffrent creators with wildly different supports and layer heights, and every one came out keeping whatever was baked into that specific 3MF. Only the machine side gets swapped over to the U1 hardware settings. If it was pulling from the first file only, I woud have caught it fast, because half that batch would have printed with the wrong supports. That said, do a cheap sanity check before committing a big run. Convert two of your files one at a time, then run those same two through a batch and compare the results. If they match, you're good to throw the whole folder at it. For the command line on Windows, a plain batch file loop works fine. The shape of it is somethig like:

for %%f in (C:\staging\*.3mf) do converter.exe %%f --out C:\ready

Check the readme for the exact flag names since they changed a bit between versions, and if any of your folder paths have spaces in them you'll need quotes around those paths. Save that line in a text file, rename it to .bat, double click, and it chews through the whole folder. If you want to get fancier later, that PowerShell setup described up above is nicer since it can watch a folder and ping you when it's done, but honestly the simple loop carried me for months. One gotcha to watch for: some 3MFs out there don't actually carry custom settings, they just inherit whatever system profile the slicer had loaded when the creator hit export. Those convert fine but there's nothing creator-dialed in them to preserve. So if one file comes out looking generic, check the source before blaming the batch mode.

One thing I'd add from my own batch runs is that even when the per-model settings carry over correctly, a couple of them can end up nonsensical on the target machine, like a taller layer height than the nozzle conversion really likes, and the tool just accepts it silently. So after the comparison test the previous poster suggested, I'd also eyeball the sliced output of one or two files before letting the whole folder loose, since a bad value that slips through quietly is worse than an outright failure. Does the tool write a log anywhere when it skips or overrides something? I've never bothered to check and now I'm curious.

One thing to add to the batch file approach: put a pause at the end of the .bat, otherwise the window closes the second it finishes and you can't see if anything errored out. I run maybe 30 or 40 conversions a week this way and that single line has saved me from blindly trusting the output more than once. Also worth giving the output folder its own name instead of dumping back into the source folder, since a couple of files with the same name from different subfolders will quietly overwrite each other. Found that out after losing a weekend's worth of slicing.

Been doing this since the days when the only option was unzipping the 3MF and hand-editing the config file in a text editor, so trust me, a batch loop is luxury. One habit I'd pick up early: never run the converter on your only copies. Keep the originals in a folder you never touch and convert into a seprate working directory. I lost a couple of files years back to an early converter version that wrote bad output and had nothing to fall back on. Version your converter too, pin the one that works and don't auto-update mid-project.

That last part about some files not actually having settings saved in them kind of worries me. I've downloaded a bunch of models and I honestly have no idea which ones the creator messed with and which ones they just hit export on. Is there a way to check a file before converting it, like opening it in something and looking, or do you only find out after it prints weird? Also thanks for the pause tip above, I would have definitely closed that window too fast without even thinking about it.

Update: ran my first real batch last night. Per-file settings held up exactly like the first reply said, supports and layer heights carried over fine. The pause tip saved me too, caught one file erroring out instead of the window vanishing. Still stuck on the silent bad settings thing though. Is there a way to make the tool flag those, or is eyeballing the comparison the only option?