In Jain dharma, two main things are seen in any act of hiṁsā:

1. Dravya-hiṁsā – actual physical injury/death caused
2. Bhāva-hiṁsā – the inner intention, fear, anger, hatred, carelessness, etc.

From what you wrote:

• You knew the bats come at night.
• You knowingly switched on the fan with the idea that “if they come out, they will be hit and then they will not be able to bite me.”

So:

1. Was this hiṁsā (violence)?

Yes, from Jain viewpoint this is hiṁsā, because:

• You were aware living beings (bats) are there.
• You accepted the possibility of their being injured/killed as a “solution” for your safety.
• So there is bhāva-hiṁsā (intention accepting their harm).

Even if no bat actually died, the intention itself binds karma. Jain texts clearly say: it is not only the outward act, but the inner bhāva that mainly binds karma. ( jainknowledge.com)

2. Is self-protection allowed?

For śrāvaks (householders), Jain dharma allows minimum necessary virodhi / self‑defence hiṁsā when there is a real threat to life, but:

• Only as last option
• With least possible harm
• Without anger, cruelty, or “let them die, so I am safe” kind of feeling

In your case, more ahimsak options were possible, for example:

• Calling wildlife control or some local service to safely remove the bats
• Sleeping in another room / closing that room till they are removed
• Using a net around your bed
• Keeping windows/doors arranged so bats can fly out safely, etc.

Because such options exist, simply letting the fan injure them is not the ideal Jain way.

3. What should you do now (prāyaścitta)?

Jain way is not to feel lifelong guilt, but to:

1. Accept inwardly: “Yes, this was a form of hiṁsā done out of fear and ignorance.”
2. Do pratikramaṇ (even simple form):

- Calmly recall the act and your intention. - With sincere feeling say (in your own language or with the idea of Micchāmi Dukkaḍaṁ): - “I regret this violence, I do not wish to repeat it. May all living beings forgive me; I forgive all.”

1. Resolve (saṅkalpa):

- “Next time, I will try to protect myself in a way that harms the least number of jīvas.”

1. If you can, support some act of compassion (feeding animals, donating for animal care, etc.) with a pure, humble intention – this helps soften the inner bhāva.

4. How to handle such situations in future

• First think: “How can I protect both – myself and other jīvas – as much as possible?”
• Prefer non‑killing solutions: nets, shifting room, gentle removal, professional help, etc. ( jainknowledge.com)
• If some level of hiṁsā becomes truly unavoidable for protection of life, keep the mind soft, without hatred, and do pratikramaṇ afterwards.

In short: Yes, what you did is counted as hiṁsā in Jain dharma, mainly because of the intention. Now, use this as a chance to purify your bhāva through pratikramaṇ and to be more careful and compassionate in similar situations ahead.