Hans,
To keep this short... I had a similar situation... total of over 100 QSLs, but less than 100 cards and less than 100 LoTW.
What did I do?   
1. Submit an application with just the cards using the online application process (not within LoTW) to add the cards to my 'legacy' account.  Note that you can submit an application that just adds the card QSLs to your legacy account even though the application includes less than 100 QSLs.
2. Once the card QSLs are processed and added to my 'legacy' account, then make sure my legacy DXCC account is linked to my LoTW DXCC account.
3. Finally, use the LoTW application process to submit an award application that will include the 'linked' legacy QSLs and the true LoTW QSLs. 
It takes a while to work through this process, but.... It does work.
73,  Rick - K5GZR