Use the scan counts and warnings to understand what PD Guard actually examined. The integrity and malware scans use related filters but have different file types and result limits.

Compare the two scan types

File Integrity compares fingerprints for PHP and PHTML files with a saved baseline. Malware Scan looks for selected code patterns in PHP, PHTML and INC files. Neither is a complete inventory of all website content or a scan of every customer’s hosted files.

Both omit library, cache, temporary, upload and other deliberately excluded trees, including recognised configured upload locations and previous-version copies. Symbolically linked files and directories are not followed. Malware scanning also excludes the PD Modules tree itself. Files in those areas are not proven safe by an empty result.

Read the relevant limit

1. Open the intended Pro scan tab and check its last-scan time.
2. Run Scan now only when you intend a new local scan.
3. Review the processed count and any cap warning.
4. Compare the displayed finding lists with their totals.

The scans have a 20,000-file limit. Malware scanning skips content above its 2,000,000-byte per-file limit, although those files can still contribute to the displayed processed count. Failed reads can also leave content unexamined without a complete separate skipped-file list.

Distinguish a partial display from a partial scan

Integrity retains bounded filename lists while preserving difference totals. Malware retains up to 300 findings and can continue counting further matches; counts are pattern matches rather than a guaranteed number of distinct infected files. A cap warning can therefore concern file coverage or finding display.

There is no general scan-root or exclusion editor in these tabs. Do not follow generic advice to narrow a root or edit internal tables as a repair. An empty result does not answer a question about excluded content. Keep the count, warning, time and redacted symptom if the displayed scope or result needs investigation.

See the PD Guard WHMCS guide for related tasks, or explore PD Guard.