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Sometimes a PDF page contains objects which are hidden by clipping paths (clips). When you edit such a PDF using Infix PDF Editor it will ask if you want to make hidden objects visible. This is needed because some PDFs routinely clip every line of text (for no good reason). If Infix didn't remove these clips then text would often become invisible after an edit.
Since TransPDF isn't interactive it automatically removes these clips to make all hidden objects visible. Most of the time this is exactly what's needed. However, there are a few PDFs which contain hidden objects - images, artwork, page numbers etc. that really should remain hidden. These may have been left in the PDF accidentally by the author.
Our development server is different in that it leaves hidden objects hidden. To take advantage of this behaviour, upload your problem PDF to transdev.iceni.com and process it there. It will take longer since it's a small development machine but it should leave the hidden objects hidden, even after translation.