Why not use https://docs.rs/regex/1.1.6/regex/fn.escape.html? If you are worried about performance you can use https://docs.rs/regex-syntax/0.6.6/regex_syntax/fn.escape_into.html which is quite fast.

It is worth putting a comment that these are matched in order.

Put doc comments before the thing that they are documenting and use ///

I suspect this .iter() isn't required.

This function appears to be way more complicated then it needs to be. I have tried to highlight the changes in comments below but I have a full version at https://rust.godbolt.org/z/08MrDP. I haven't actually run the code but I think my version has the same functionality as this one.

If you are worried about performance you can use a buffer outside the loop and replace it with line.replace_range(.., line_str). This saves continuously reallocating the string.

This copy is unnecessary and having the lifetime start so early is confusing. The only time this is used is as a temporary in the syntax: case and to set line_syntax where it is always unchanged from the default. This variable should just be removed.

This is also unnecessary. Because of the above comment.

You can just call str methods on String because they implement Deref<str>.

line = line.as_ref().trim_end().to_string();

rel_syntax: &'static str so this can be Cow::Borrowed. Actually current_syntax is only ever set to static lifetime strings so you don't have to use Cow at all.

This clone is unnecessary it is always a reference to line from herein so you can just use &str.

Slight preference for format!(). In theory it can do clever things like checking argument sizes to only allocate once. Either way I think it looks nice.

I'm pretty sure this is redundant because the only time syntax is modified is in the syntax: case which A) Sets current_syntax and B) continues.

Mapping to an always-ok result is odd. You should just map to the parse_pattern_file_contents(). Then you don't need to use ? to unwrap the extra layer. However you then loose the error conversion which you can add back with .map_err(|e| e.into()).

https://rust.godbolt.org/z/Mflpga

Even better is just use the try for the read and call parse_pattern_file_contents at the function level.

f.read_to_string(&mut contents)?;
Ok(parse_pattern_file_contents(&contents, &file_path, warn))

This seems like overkill to me. I would either remove it or use pub struct LineNumber(pub usize) if you want to do this for type safety. However I don't think type safety is really needed here so I would just remove the alias.