Full Conversion vs Custom Stories?

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There are significant and insignificant differences between a full conversion and a regular custom story. Significant differences deal with adjusting game mechanics by editing configuration files. Insignificant differences deal with the ability to adjust presentation of your custom story (e.g. pre-menu, main menu, loading screen image, fonts, etc). The reason why a full conversion is recommended for flashlights is simply to avoid overwriting the original Amnesia content. Do note that full conversions have the tendency of being problematic or inconvenient to the user (and sometimes the developer), so unless you really need to (i.e. touch on mostly the significant reasons stated here), you should consider a regular custom story over a full conversion.