This procedure is strongly recommended on all devices on iOS 4 or lower, not jailbroken with Legacy iOS Kit. This also assumes you aren't able to use Legacy iOS Kit.
There is a bug with newer versions of Cydia Substrate that causes the touchscreen to become unresponsive when in Safe Mode. This bug is especially problematic on devices without volume buttons, as you can't boot into no Substrate mode, thus requiring you to restore.
1. Download the Cydia Substrate and Substrate Safe Mode .deb files.
2. Install iFile on your iOS device by searching it in Cydia.
3. Tap the Wi-Fi button on the bottom toolbar.
4. Take note of the last lines of the console. It should say something like "Accepting connections at http://[devicename]-local:10000 or http://[IP address]:10000".
5. Input either address into the web browser of your computer or phone, and it should show you the folders of your iOS device.
6. Open the "var" folder, then the "mobile" folder.
7. Press "Choose File" then select one of the .deb files you downloaded, then press "Upload", then navigate back in your browser. Repeat the process for the other file.
8. Press "Close" on your iOS device, then refresh the page by swiping up on the page.
9. The .deb files you transfered should be there. Tap on one and press "Installer", then do the same for the other.
10. Restart your iOS device.
You have now successfully downgraded Cydia Substrate, preventing the bug. Cydia may notify you to update the tweaks, which you can ignore by opening the tweak page, pressing "Configure" then enabling "Ignore All Changes" for both of them.