Seeing that this didn't worked, I purged the PPA using ppa-purge and had to reinstall the flatpak package from the repos.
Since then, I can't either find flatpaks using the Software Manager, nor can I install them from the Flathub by opening the flatpakref packages with it.
Installing Flatpaks still work on the terminal, however.
Another thing to note is that I purged the flatpak package before upgrading to Mint 20.3 and, only now, I've noticed the bug. I don't think this caused it, but thought it might be good to know.
inxi -Fxxxrz
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System: Kernel: 5.4.0-96-generic x86_64 bits: 64 compiler: gcc v: 9.3.0 Desktop: Cinnamon 5.2.7 wm: muffin
dm: LightDM 1.30.0 Distro: Linux Mint 20.3 Una base: Ubuntu 20.04 focal
Machine: Type: Laptop System: Avell High Performance product: A60 MUV v: N/A serial: <filter> Chassis: type: 10 v: 1.0
serial: <filter>
Mobo: Avell High Performance model: Avell High Performance serial: <filter> UEFI: Intel
v: QCCFL357.0122.2020.0911.1520 date: 09/11/2020
Battery: ID-1: BAT0 charge: 58.1 Wh condition: 58.1/93.5 Wh (62%) volts: 13.0/11.4 model: standard type: Li-ion
serial: <filter> status: Full
CPU: Topology: 6-Core model: Intel Core i7-9750H bits: 64 type: MT MCP arch: Kaby Lake rev: A L2 cache: 12.0 MiB
flags: avx avx2 lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx bogomips: 62399
Speed: 3967 MHz min/max: 800/4500 MHz Core speeds (MHz): 1: 3981 2: 3920 3: 3983 4: 3988 5: 3980 6: 3988 7: 3990
8: 4020 9: 3989 10: 3981 11: 3989 12: 3966
Graphics: Device-1: Intel UHD Graphics 630 driver: i915 v: kernel bus ID: 00:02.0 chip ID: 8086:3e9b
Device-2: NVIDIA TU116M [GeForce GTX 1660 Ti Mobile] vendor: Intel driver: nvidia v: 470.86 bus ID: 01:00.0
chip ID: 10de:2191
Display: x11 server: X.Org 1.20.13 driver: modesetting,nvidia unloaded: fbdev,nouveau,vesa
resolution: 1920x1080~144Hz
OpenGL: renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2 v: 4.6.0 NVIDIA 470.86 direct render: Yes
Audio: Device-1: Intel Cannon Lake PCH cAVS driver: snd_hda_intel v: kernel bus ID: 00:1f.3 chip ID: 8086:a348
Device-2: NVIDIA TU116 High Definition Audio vendor: Tongfang Hongkong Limited driver: snd_hda_intel v: kernel
bus ID: 01:00.1 chip ID: 10de:1aeb
Sound Server: ALSA v: k5.4.0-96-generic
Network: Device-1: Realtek RTL8111/8168/8411 PCI Express Gigabit Ethernet vendor: Intel driver: r8169 v: kernel port: 3000
bus ID: 3d:00.0 chip ID: 10ec:8168
IF: enp61s0 state: down mac: <filter>
Device-2: Intel Wi-Fi 6 AX200 driver: iwlwifi v: kernel port: 3000 bus ID: 3e:00.0 chip ID: 8086:2723
IF: wlp62s0 state: up mac: <filter>
IF-ID-1: docker0 state: down mac: <filter>
Drives: Local Storage: total: 476.94 GiB used: 345.38 GiB (72.4%)
ID-1: /dev/nvme0n1 vendor: A-Data model: IM2P33F8BR2-512GB size: 476.94 GiB speed: 31.6 Gb/s lanes: 4
serial: <filter> rev: T0214B0L scheme: GPT
Partition: ID-1: / size: 97.93 GiB used: 35.73 GiB (36.5%) fs: ext4 dev: /dev/nvme0n1p5
Sensors: System Temperatures: cpu: 82.0 C mobo: 82.0 C gpu: nvidia temp: 61 C
Fan Speeds (RPM): N/A
Repos: No active apt repos in: /etc/apt/sources.list
Active apt repos in: /etc/apt/sources.list.d/additional-repositories.list
1: deb http://deb.tuxedocomputers.com/ubuntu focal main
2: deb [arch=amd64,armhf,arm64] https://packages.microsoft.com/ubuntu/20.04/mssql-server-2019 focal main
No active apt repos in: /etc/apt/sources.list.d/alexlarsson-flatpak-focal.list
Active apt repos in: /etc/apt/sources.list.d/geogebra.list
1: deb http://www.geogebra.net/linux/ stable main
Active apt repos in: /etc/apt/sources.list.d/google-chrome.list
1: deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main
No active apt repos in: /etc/apt/sources.list.d/lutris-team-lutris-focal.list
No active apt repos in: /etc/apt/sources.list.d/mattrose-terminator.list
Active apt repos in: /etc/apt/sources.list.d/microsoft-prod.list
1: deb [arch=amd64] https://packages.microsoft.com/ubuntu/20.04/prod focal main
Active apt repos in: /etc/apt/sources.list.d/official-package-repositories.list
1: deb http://packages.linuxmint.com una main upstream import backport #id:linuxmint_main
2: deb http://archive.ubuntu.com/ubuntu focal main restricted universe multiverse
3: deb http://archive.ubuntu.com/ubuntu focal-updates main restricted universe multiverse
4: deb http://archive.ubuntu.com/ubuntu focal-backports main restricted universe multiverse
5: deb http://security.ubuntu.com/ubuntu/ focal-security main restricted universe multiverse
6: deb http://archive.canonical.com/ubuntu/ focal partner
Active apt repos in: /etc/apt/sources.list.d/vscode.list
1: deb [arch=amd64,arm64,armhf] http://packages.microsoft.com/repos/code stable main
Info: Processes: 409 Uptime: 2h 40m Memory: 15.48 GiB used: 3.99 GiB (25.7%) Init: systemd v: 245 runlevel: 5 Compilers:
gcc: 9.3.0 alt: 9 Shell: zsh v: 5.8 running in: guake inxi: 3.0.38