How to change line endings from Windows to Unix
In FTP by Zaweba, choose Convert to LF (Unix / web servers) on the editor's status-bar menu to switch a file from Windows CRLF to Unix line endings.

Open the file in FTP by Zaweba's editor and use Convert to LF (Unix / web servers) from the menus on the status bar. Save, and the file now has Unix line endings. To go the other way, Convert to CRLF (Windows) is beside it.
The status bar also tells you which line endings a file has right now, so you can check before and after.
What line endings are
Every line of a text file ends with an invisible marker. Windows traditionally uses two characters, a carriage return and a line feed, called CRLF. Unix, Linux and macOS use just the line feed, called LF. Most web servers run Linux, so LF is what they expect.
Most of the time it doesn't matter. Browsers read HTML, CSS and JavaScript happily either way. But some things are fussy: shell scripts on a Linux server can fail with CRLF, some configuration files misbehave, and mixing both in one project makes diffs and version control noisy, with every line appearing changed when only the endings are.
Converting a file
Open the file from the local or server pane. Look at the status bar; alongside the language and encoding, it shows the current line endings.
Open the line-ending menu on the status bar and choose Convert to LF (Unix / web servers).
Save the file. If Upload on Save is on for the site, it goes straight up to the server; otherwise upload it with Put.
Check the status bar again to confirm the change.
Why the editor doesn't change them on its own
FTP by Zaweba keeps a file's encoding and line endings byte-exact when you save. That's deliberate. An editor that quietly converts files can produce a long list of "changed" files that you never really changed, and it can break the occasional file that depends on its exact bytes. So conversion only happens when you ask for it.
That also means you can edit a CRLF file and leave it CRLF, if that's what it needs to be.
Spotting the difference in a comparison
If a file shows as different from the server copy but looks identical, line endings are a likely cause. Compare with Server Copy on the right-click menu opens a diff window; Ignore whitespace can help you see whether the real content differs. Once you know, convert one side to match.
Encoding is the other half
Line endings and encoding are often confused because they cause similar mystery problems. Encoding is how the characters themselves are stored. The same status-bar area lets you save as UTF-8, UTF-8 with BOM, UTF-16 LE or ANSI. For web files, UTF-8 is the usual choice.
A good habit
Pick one convention for a site, usually LF for anything that lives on a Linux server, and convert files as you open them for other reasons rather than all at once. You'll keep diffs readable and never be surprised by a script that fails for no visible reason. FTP by Zaweba keeps local version history of files it overwrites, so if a conversion ever causes trouble, the previous version is there to restore.