Even after increasing the open file limit as described here Too many open files error, it does not prevent Confluence to crash.
Actually, the issue is based on the Confluence platform itself even though it appears that the Linchpin Theme app is involved.
The data storage of the logo which is uploaded via the Linchpin theme configuration (/admin/linchpin/theme/configure.action) is always a Base64-encoded string, i.e. it is not a file nor attachment and ultimately not stored in the file system.
However, the Linchpin theme also sets the regular site logo of Confluence as well using a standard Confluence API method. That site logo can be seen even without an active or applied Linchpin theme (e.g. in the admin area on the top left). As a matter of fact, that Confluence site logo is an attachment file, i.e. a file in the file system which can be affected by the stated issue.