Just a while ago I was having issues with SimpleLSiOS where I played around with its settings then it insta-crashed my phone to Safe Mode. I respring and it still booted my phone into Safe Mode. Reinstalling through Cydia didn't work since it retained my configuration preferences. But this is what I can share!

If, whatever reason, a tweak crashes your phone to safe mode after a poor configuration change through its settings, this is what you can do! (I've only tried this on iOS 10.3.1 so directories may be different on other iOSes. And please ensure you have Apple File Conduit "2" installed to access the Jailbreak directories, I had to when using iTools.)

1.) Access some file viewer as in Filza, iFunbox, iTools, etc.

2.) Go to /Library/MobileSubstrate/DynamicLibraries/

3.) Locate the tweak's .plist file

4.) Rename it - I like to add an "x" in front of it for simplicity

5.) Respring your phone, this should kick your phone out of Safe Mode

6.) Go to Settings and try your best to undo the last change or manually (undo) all the tweak's configuration back to default

7.) Rename the .plist back to its original name

8.) Respring phone! It should now be able to work out of Safemode and your tweak can be modified again.

Hope this helps!