It's not really provable what software got used to create a file. Well, depends on the file format but like I mentioned you simply could resave everything with legal software to make sure any possible traces are removed.
If you get sued (but why?) the police could theoretically come and check all software you have installed on your computer for valid licenses.
This ia a very important issue for all " poor artist " Indie game programmers
Take for example XSI MOD Tool and XSI 7.5 by Softimage
How can the american " pirate watchdog agencies " distinguish files exported from these applications ?
Do they contain a " flag " or a "structure " as a trace ?
If so, is it sufficient to resave the file with legal software ?
I purchased several models from eastern european and far east arttis where the use of illegal software, no offence , is the normality