Ditto on Jim's comments. Here is the likely scenario. Owner ran first payroll in April, MAS screamed and would let the update proceed. Owner got distracted so he/she just opened the PR setup options, flipped the quarter to 2 and updated the PR in April. Could luck in getting a confession. Maybe the PR audit file will shine the light but I think this only works in company maintenance.
Personally, I wouldn't bother with fixing the MAS files. The only buckets are QTD and YTD. The YTD are fine and as soon as you close 2nd quarter, so wil the QTD buckets. You have to manually calculate the numbers anyway for the 941 so just download a PDF from the IRS and enter the numbers on that form. The big unknown is the SUTA wages by employee. For these amounts, I would do a query in the PR perpetual history (hopefully, this is turned on). Then use an Excel Pivot table to summarize by employee by quarter. Actually, this is where a good backup from the 1st quarter would be VERY handy.