Save a Copy as... with the clone option under no circumstances will delete records from the original copy.
However, filemaker uses Save a copy as... a bit different from some other common applications and this difference can fool you into thinking that this is what happened.
When you save a copy with filemaker, the original copy of the file remains open and new copy of the database is created at the location you specify with the name you enter. If you save a copy with other applications such as MS Word, the newly saved copy is the open copy and the original is now closed. This difference has fooled others in this manner before and is likely the explanation of what you observed.
Try this again with a copy of your file and note watch how the file name of your open copy does not change like it does with most other applications.
I experienced the same/a similar situation today.
Made a clone of a (very) important file because I wanted to start over the numbering again.
At least..I thought I made a clone. Although I choose "save a copy as clone" FileMaker produced" a new file (with a new name I gave it) but wich retained all the records in it. No matter how many times I tried, FM did not make a clone but instead made a copy.
So I thought, "OK than, then I make a "clone" myself manualy and I erase all the records". "What could happen!? I have a copy a the file and it has another name".
So I erase all records just to find out that all records in the original files have been erased to. Suprise!
Lucky for me the back up system that was down for some time (without me knowing it) was again up and running since...yesterday!
Probably this happens because it is a rather "complicated" file with relatioships to other files.
Any tips on this issue would be welcome.