Fix unrepresentable characters before exporting an EPUB. First resolve the manuscript's encoding problem; only then investigate navigation, images, and package structure. Treating every garbled character as an EPUB defect can lead you to change correct book settings while the real damage remains in the source file.
Distinguish encoding from font display
A question mark or empty box can come from several layers: the chosen encoding cannot represent the character, the file was decoded incorrectly, or the display font lacks a glyph. Duplicate the source and record a known sentence plus each suspicious position before changing anything.
Consider a three-chapter manuscript inherited from Shift_JIS with two emoji. Determine whether the delivery requirement allows UTF-8. If it does, converting the copied source may preserve the intended characters. If it does not, the author must choose meaningful replacements. Never overwrite the only source while its decoding is uncertain.
Use Rune Studio's per-file encoding controls carefully
Rune Studio can read UTF-8 with or without BOM, Shift_JIS, EUC-JP, ISO-2022-JP, UTF-16LE, UTF-16BE, and a final fallback. Encoding and line ending can be changed from the status bar. The documented Mac behavior marks Unicode ranges that the selected encoding cannot represent, pauses autosave while they remain, and warns during save.
Read the current encoding in the status bar, navigate to the suspicious characters, and retain an untouched copy. Correct the characters or choose UTF-8, then reread a representative sentence, chapter headings, and each changed location. Save under a recoverable name, reopen it, and check that the line ending did not change unintentionally.
Export only after the text layer is clean
Once all three sources are readable and no conversion issue remains, proceed to File Selection and Chapter Order in the EPUB wizard. Navigation and image checks now address the package rather than masking a source-encoding failure.
In the available operation run, a character that caused a conversion failure was corrected and the subsequent EPUB passed its local structural check. Another encoding check set the tab to UTF-8 with LF and found no unconvertible character on reinspection. The same run did not visually verify Rune Studio's red background or the paused-autosave indicator.
Keep the unobserved UI out of the success claim
The documented warning behavior and the measured repair-and-export result are therefore separate evidence. If the visible warning is important to your decision, reproduce it in a disposable copy and observe the editor before relying on it. Do not rewrite “not visually checked” as “confirmed on screen.”
External readers and retailers may apply their own processing, so inspect names, emoji, and uncommon glyphs in the destination preview as a later step. Rune Studio's current encoding support defines the product scope; your safest first action is reopening one converted chapter before exporting the whole book.
