That's perfectly fine, even if you use the same wallets (created from the same seeds) on both systems.
nerioseole alluded to one above—Electrum 2.x uses a different wallet format. If you give it a 1.9.8 wallet file, it will upgrade it to the new format behind the scenes (the seed remains the same). If you ever want to copy this 2.x wallet file to a machine that has Electrum 1.x on it, you'll need to instead either:
- Use a backup from Electrum 1.x, or
- simply restore from the seed.