Build directory not initialized, use flatpak build-init

I’m trying to build an update to a flatpak and I’m getting a weird error I’ve never seen before. It’s a fresh build and the error occurs in the first module of the manifest:

⬢[fede@toolbox org.frescobaldi.Frescobaldi]$ flatpak-builder build --force-clean --install --user org.frescobaldi.Frescobaldi.yaml 
Emptying app dir 'build'
Downloading sources
Starting build of org.frescobaldi.Frescobaldi
Cache miss, checking out last cache hit
fuse: unknown option(s): `-o splice_write,splice_move'
Building module guile in /var/home/fede/src/
Applying patch guile-1.8.8-deplibs.patch
patching file
patching file guile-config/
patching file libguile/
Hunk #2 succeeded at 2126 (offset -5 lines).
Hunk #3 succeeded at 2148 (offset -5 lines).
Applying patch guile-1.8.8-cve-2016-8605.patch
patching file libguile/filesys.c
Hunk #1 succeeded at 791 (offset -464 lines).
Applying patch guile-1.8.8-configure.patch
patching file
patching file configure
error: Build directory /var/home/fede/src/ not initialized, use flatpak build-init
Error: module guile: Child process exited with code 1

As you can see above, I’m running flatpak-builder in a toolbox container.
I removed the build/ and .flatpak-builder/ directories before launching the command.

In flatpak tracker I’ve read that weird errors might be caused by a faulty manifest file. My manifest is passing the yamllint check and I can’t see any error. What I’ve done so far is in this branch:

I have a lot of disk space…

What else should I check?
Thanks in advance.

Today the build started normally.
Before launching it I did a sudo dnf upgrade in the toolbox container, but there was no upgrade of any flatpak package. Weird…