How can the use of separators in PHP affect the functionality of cookies?

Using separators in PHP can affect the functionality of cookies because some characters used as separators, such as commas or semicolons, are reserved characters in cookies and can interfere with the parsing of cookie values. To solve this issue, it is recommended to use a different separator that is not a reserved character in cookies, such as a pipe "|" or a colon ":".

```php
// Set cookie with custom separator
$cookie_value = "value1|value2|value3";
setcookie("my_cookie", $cookie_value, time() + 3600, "/");
```
In this code snippet, we are setting a cookie named "my_cookie" with a custom separator "|" between the values "value1", "value2", and "value3". This avoids using reserved characters like commas or semicolons as separators.