This then would be a "disclaimer of opinion", not a valid reason for the auditor to withhold or not sign the reports. From the instructions for Form 5500, Schedule H, Line 3a(3), "Check if a disclaimer of opinion was issued. A disclaimer of opinion is issued when the IQPA is unable to obtain sufficient appropriate audit evidence on which to base the opinion, and the IQPA concludes that the possible effects on the financial statements of undetected misstatements, if any, could be both material and pervasive."
This is why this category originally existed, when the auditor couldn't timely, or ever, obtain all the materials it thought was needed, or prove that there was actual wrong-doing and to what effect it impacted the participants. The limited-scope use of this category has become the default, and most audits are physically performed by junior associates who may not have any experience otherwise.
Obviously the reports would be full of warnings and whatever notes the auditors wish to include, and management may also include a rebuttal letter of explanation to the audit report if they so desired. But it is not an excuse not to issue the report, if they are reluctant to do so for reasons not supported by SAS 136, fire them for breach, and hire someone who understands the situation and is willing to work with what you have available.