Sophisticated Core v1.3.25 (initially) and also v1.3.34
Sophisticated Storage v1.4.19 (initially) and also v1.4.26

Items are being deleted from the Sophisticated Storage double chests when they are pumped into the chest from the right side but this only happens if the pipe is on the right side and the double chest is formed with the right side first and then the left side of the chest placed. This has been tested with multiple pipes such as Mekanism logistical transporter and the Modern Dynamics item pipes. This bug happens with all tiers of the Sophisticated Storage chests.

Start with no chest and an item pipe on the right side:

Place first chest against pipe with pipe on right side:

Place second chest on left and it forms a double chest:

Then after that it will delete all input into that chest once you start pumping in items. Breaking the left chest causes the remaining right side to work again but replacing the left side continues deleting items.

Thanks for reporting this. Apparently I was not invalidating item capabilities when the chest combined into double chest so the pipe would have the capability of single chest cached and would continue inserting into non existent single chest. Just pushed a release with fix for this (invalidates capabilities when chest combines into double chest and so any blocks that have this capability cached should get a new correct one). Release should be approved on curseforge / modrinth shortly.