You'll need to change the sub-selects to query against tblFileVersions instead of tblSoftware. The approach is the same: create a query to check whether file X has been scanned for and/or found; create a second query to check whether file Y has been scanned for and/or found. Those are your sub-selects. Link the main select of your assets against those two.
e.g.
Select Top 1000000
tblAssets.AssetID,
tblAssets.AssetName,
tsysAssetTypes.AssetTypename,
tsysAssetTypes.AssetTypeIcon10 As icon,
tblAssets.IPAddress,
tblAssets.Lastseen,
tblAssets.Lasttried,
softwareX.FileStatus AS X_status,
softwareX.FilePathfull AS X_name,
softwareX.FileVersion AS X_version,
softwareY.FileStatus AS Y_status,
softwareY.FilePathfull AS Y_name,
softwareY.FileVersion AS Y_version
From
tblAssets
Inner Join tblAssetCustom On tblAssets.AssetID = tblAssetCustom.AssetID
Inner Join tsysAssetTypes On tsysAssetTypes.AssetType = tblAssets.Assettype
Inner Join tblComputerSystem On tblComputerSystem.AssetID = tblAssets.AssetID
Left Join (SELECT
tblFileVersions.AssetID,
Case tblFileVersions.Found
When 0 Then 'Absent'
When 1 Then 'Present'
Else '(not checked)'
END AS FileStatus,
tblFileVersions.FilePathfull,
tblFileVersions.FileVersion,
tblFileVersions.CompanyName
FROM
tblFileVersions
WHERE
tblFileVersions.FilePathfull Like '%file_1%') AS softwareX On softwareX.AssetID = tblAssets.AssetID
Left Join (SELECT
tblFileVersions.AssetID,
Case tblFileVersions.Found
When 0 Then 'Absent'
When 1 Then 'Present'
Else '(not checked)'
END AS FileStatus,
tblFileVersions.FilePathfull,
tblFileVersions.FileVersion,
tblFileVersions.CompanyName
FROM
tblFileVersions
WHERE
tblFileVersions.FilePathfull Like '%file_2%') AS softwareY On softwareY.AssetID = tblAssets.AssetID
Where
tblAssetCustom.State = 1 -- active
AND tblAssets.AssetType = -1 -- Windows machines
AND tblComputerSystem.Domainrole <= 1 -- workstations
AND softwareX.FileStatus IN ('Present', '(not checked)') -- file 1 found or not yet checked for
AND (softwareY.AssetID IS NULL
OR SoftwareY.FileStatus IN ('Absent', '(not checked)') ) -- file 2 not found or not yet checked for