Hello
I opened a new project in Arduino IDE 1.8.13 on Arch linux, wrote some code in it and saved it to the default location, ending up with a project called something like sketch_nov06b.ino.
I wanted to overwrite an old project I had, as this code did the same job but better. I clicked "File -> Save As...", and saved it as a dot ino file that already existed. I was prompted that this would delete the old dot ino file, which I was ok with. In addition to deleting the dot ino file, it deleted the whole folder, with all the data in it, and created a new folder with the same name containing nothing but the new ino file.

Steps to reproduce

Have a folder with a sketch and some important data.

$ pwd
/home/haavagj/git/test_project
$ ls
important_data.txt important_data.txt~ test_project.ino test_project.ino~ 
$ cat test_project.ino
void setup() {
 // put your setup code here, to run once:
 unimportand_code();
}
void loop() {
 // put your main code here, to run repeatedly:
 more_unimportant_code();
}

Overwrite test_project.ino with Arduino IDE 1.8.13 on Arch linux and lose important data.

$ ls
ls: reading directory '.': No such file or directory
$ pwd
/home/haavagj/git/test_project
$ cd ../test_project 
$ ls
test_project.ino
$ cat test_project.ino 
void setup() {
 // put your setup code here, to run once:
 improved_setup();
}
void loop() {
 // put your main code here, to run repeatedly:
 improved_loop();
}