It is possible to edit certain mods so that they're compatible with the new update, but it all depends on how much you know regarding the game's files and what kind of mods you wish to use. If you're using the current items and markings pack as Morqque said, then there shouldn't be a problem unless you've installed them wrong. Other mods such as the GUI interfaces can have problems with the new update, but they can be edited so that they work, which is what had to happen with my custom interface after the update.
Which markings and items pack are you using? If you're not using the legendary packs then that could be the reason they're not working for you.