Let me tell you how I did it so far.
We are a amateur orchestra who has almost every sheet of music digital (pdf). For now the archive is 3,5 Gb with over 3300 sheets. The size of the pdf's are different. The conductor sheets are the largest. From 4Mb to almost 70 Mb. For each musician the files are from 300 Kb to 15 Mb.
But the problem did not occur with the larger files so far.
Download directory Monitoring is set Yes, but I understand with these number of files it is better to set it to No.
I upload the files using ftp (FileZilla) because of the numbers of files to upload.
So now I changed the Download Monitoring to No and uploaded a new number of files (133). After that I went to the Control panel and at Status Monitoring I did a Check Download area now (manually).
All went fine now and it gave no problems at all.
So I would say, you solved my problem. Great thx.